data_7LJY # _entry.id 7LJY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7LJY pdb_00007ljy 10.2210/pdb7ljy/pdb WWPDB D_1000254525 ? ? EMDB EMD-23401 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2021-04-14 2 'Structure model' 1 1 2024-03-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' refine # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_refine.ls_d_res_high' 4 2 'Structure model' '_refine.ls_d_res_low' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7LJY _pdbx_database_status.recvd_initial_deposition_date 2021-02-01 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB . EMD-23401 'associated EM volume' EMDB . EMD-23402 'other EM volume' # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Torabi, S.' 1 ? 'Chen, Y.' 2 ? 'Zhang, K.' 3 ? 'Wang, J.' 4 ? 'DeGregorio, S.' 5 ? 'Vaidya, A.' 6 ? 'Su, Z.' 7 ? 'Pabit, S.' 8 ? 'Chiu, W.' 9 ? 'Pollack, L.' 10 ? 'Steitz, J.' 11 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 118 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Structural analyses of an RNA stability element interacting with poly(A).' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.2026656118 _citation.pdbx_database_id_PubMed 33785601 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Torabi, S.F.' 1 0000-0003-1643-3583 primary 'Chen, Y.L.' 2 0000-0002-1285-069X primary 'Zhang, K.' 3 0000-0003-0414-4776 primary 'Wang, J.' 4 0000-0002-4504-8038 primary 'DeGregorio, S.J.' 5 ? primary 'Vaidya, A.T.' 6 ? primary 'Su, Z.' 7 0000-0002-9279-1721 primary 'Pabit, S.A.' 8 0000-0002-2102-2474 primary 'Chiu, W.' 9 0000-0002-8910-3078 primary 'Pollack, L.' 10 0000-0002-9366-4396 primary 'Steitz, J.A.' 11 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'B dENE construct' 24242.186 1 ? ? ? ? 2 polymer syn 'poly(A)' 9172.806 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GGGUACUCUUUUCUUUGUCAUGGUUUUCUCAGGCGAAAGUCUGAGUUUUUACAUGACAAAGUUUUUAACGAGGCCC GGGUACUCUUUUCUUUGUCAUGGUUUUCUCAGGCGAAAGUCUGAGUUUUUACAUGACAAAGUUUUUAACGAGGCCC B ? 2 polyribonucleotide no no AAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAA A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 G n 1 4 U n 1 5 A n 1 6 C n 1 7 U n 1 8 C n 1 9 U n 1 10 U n 1 11 U n 1 12 U n 1 13 C n 1 14 U n 1 15 U n 1 16 U n 1 17 G n 1 18 U n 1 19 C n 1 20 A n 1 21 U n 1 22 G n 1 23 G n 1 24 U n 1 25 U n 1 26 U n 1 27 U n 1 28 C n 1 29 U n 1 30 C n 1 31 A n 1 32 G n 1 33 G n 1 34 C n 1 35 G n 1 36 A n 1 37 A n 1 38 A n 1 39 G n 1 40 U n 1 41 C n 1 42 U n 1 43 G n 1 44 A n 1 45 G n 1 46 U n 1 47 U n 1 48 U n 1 49 U n 1 50 U n 1 51 A n 1 52 C n 1 53 A n 1 54 U n 1 55 G n 1 56 A n 1 57 C n 1 58 A n 1 59 A n 1 60 A n 1 61 G n 1 62 U n 1 63 U n 1 64 U n 1 65 U n 1 66 U n 1 67 A n 1 68 A n 1 69 C n 1 70 G n 1 71 A n 1 72 G n 1 73 G n 1 74 C n 1 75 C n 1 76 C n 2 1 A n 2 2 A n 2 3 A n 2 4 A n 2 5 A n 2 6 A n 2 7 A n 2 8 A n 2 9 A n 2 10 A n 2 11 A n 2 12 A n 2 13 A n 2 14 A n 2 15 A n 2 16 A n 2 17 A n 2 18 A n 2 19 A n 2 20 A n 2 21 A n 2 22 A n 2 23 A n 2 24 A n 2 25 A n 2 26 A n 2 27 A n 2 28 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 76 'Oryza sativa' rice 4530 ? 2 1 sample 1 28 'synthetic construct' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G B . n A 1 2 G 2 2 2 G G B . n A 1 3 G 3 3 3 G G B . n A 1 4 U 4 4 4 U U B . n A 1 5 A 5 5 5 A A B . n A 1 6 C 6 6 6 C C B . n A 1 7 U 7 7 7 U U B . n A 1 8 C 8 8 8 C C B . n A 1 9 U 9 9 9 U U B . n A 1 10 U 10 10 10 U U B . n A 1 11 U 11 11 11 U U B . n A 1 12 U 12 12 12 U U B . n A 1 13 C 13 13 13 C C B . n A 1 14 U 14 14 14 U U B . n A 1 15 U 15 15 15 U U B . n A 1 16 U 16 16 16 U U B . n A 1 17 G 17 17 17 G G B . n A 1 18 U 18 18 18 U U B . n A 1 19 C 19 19 19 C C B . n A 1 20 A 20 20 20 A A B . n A 1 21 U 21 21 21 U U B . n A 1 22 G 22 22 22 G G B . n A 1 23 G 23 23 23 G G B . n A 1 24 U 24 24 24 U U B . n A 1 25 U 25 25 25 U U B . n A 1 26 U 26 26 26 U U B . n A 1 27 U 27 27 27 U U B . n A 1 28 C 28 28 28 C C B . n A 1 29 U 29 29 29 U U B . n A 1 30 C 30 30 30 C C B . n A 1 31 A 31 31 31 A A B . n A 1 32 G 32 32 32 G G B . n A 1 33 G 33 33 33 G G B . n A 1 34 C 34 34 34 C C B . n A 1 35 G 35 35 35 G G B . n A 1 36 A 36 36 36 A A B . n A 1 37 A 37 37 37 A A B . n A 1 38 A 38 38 38 A A B . n A 1 39 G 39 39 39 G G B . n A 1 40 U 40 40 40 U U B . n A 1 41 C 41 41 41 C C B . n A 1 42 U 42 42 42 U U B . n A 1 43 G 43 43 43 G G B . n A 1 44 A 44 44 44 A A B . n A 1 45 G 45 45 45 G G B . n A 1 46 U 46 46 46 U U B . n A 1 47 U 47 47 47 U U B . n A 1 48 U 48 48 48 U U B . n A 1 49 U 49 49 49 U U B . n A 1 50 U 50 50 50 U U B . n A 1 51 A 51 51 51 A A B . n A 1 52 C 52 52 52 C C B . n A 1 53 A 53 53 53 A A B . n A 1 54 U 54 54 54 U U B . n A 1 55 G 55 55 55 G G B . n A 1 56 A 56 56 56 A A B . n A 1 57 C 57 57 57 C C B . n A 1 58 A 58 58 58 A A B . n A 1 59 A 59 59 59 A A B . n A 1 60 A 60 60 60 A A B . n A 1 61 G 61 61 61 G G B . n A 1 62 U 62 62 62 U U B . n A 1 63 U 63 63 63 U U B . n A 1 64 U 64 64 64 U U B . n A 1 65 U 65 65 65 U U B . n A 1 66 U 66 66 66 U U B . n A 1 67 A 67 67 67 A A B . n A 1 68 A 68 68 68 A A B . n A 1 69 C 69 69 69 C C B . n A 1 70 G 70 70 70 G G B . n A 1 71 A 71 71 71 A A B . n A 1 72 G 72 72 72 G G B . n A 1 73 G 73 73 73 G G B . n A 1 74 C 74 74 74 C C B . n A 1 75 C 75 75 75 C C B . n A 1 76 C 76 76 76 C C B . n B 2 1 A 1 1 1 A A A . n B 2 2 A 2 2 2 A A A . n B 2 3 A 3 3 3 A A A . n B 2 4 A 4 4 4 A A A . n B 2 5 A 5 5 5 A A A . n B 2 6 A 6 6 6 A A A . n B 2 7 A 7 7 7 A A A . n B 2 8 A 8 8 8 A A A . n B 2 9 A 9 9 9 A A A . n B 2 10 A 10 10 10 A A A . n B 2 11 A 11 11 11 A A A . n B 2 12 A 12 12 12 A A A . n B 2 13 A 13 13 13 A A A . n B 2 14 A 14 14 14 A A A . n B 2 15 A 15 15 15 A A A . n B 2 16 A 16 16 16 A A A . n B 2 17 A 17 17 17 A A A . n B 2 18 A 18 18 18 A A A . n B 2 19 A 19 19 19 A A A . n B 2 20 A 20 20 20 A A A . n B 2 21 A 21 21 21 A A A . n B 2 22 A 22 22 22 A A A . n B 2 23 A 23 23 23 A A A . n B 2 24 A 24 24 24 A A A . n B 2 25 A 25 25 25 A A A . n B 2 26 A 26 26 ? ? ? A . n B 2 27 A 27 27 ? ? ? A . n B 2 28 A 28 28 ? ? ? A . n # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B C 69 ? C2 ? A C 69 C2 2 1 Y 1 B C 69 ? O2 ? A C 69 O2 3 1 Y 1 B C 69 ? N3 ? A C 69 N3 4 1 Y 1 B C 69 ? C4 ? A C 69 C4 5 1 Y 1 B C 69 ? N4 ? A C 69 N4 6 1 Y 1 B C 69 ? C5 ? A C 69 C5 # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name REFMAC _software.os ? _software.os_version ? _software.type ? _software.version 5.8.0258 _software.pdbx_ordinal 1 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 7LJY _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LJY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7LJY _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] -28.05 _refine.aniso_B[1][2] -1.78 _refine.aniso_B[1][3] -14.17 _refine.aniso_B[2][2] 8.86 _refine.aniso_B[2][3] 8.58 _refine.aniso_B[3][3] 19.19 _refine.B_iso_max ? _refine.B_iso_mean 79.714 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.945 _refine.correlation_coeff_Fo_to_Fc_free 0.885 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 7LJY _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 5.6 _refine.ls_d_res_low 5.6 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 4078 _refine.ls_number_reflns_R_free 279 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 100.00 _refine.ls_percent_reflns_R_free 6.4 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.44410 _refine.ls_R_factor_R_free 0.45134 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.44358 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 2.176 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML 110.550 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id 1 _refine_hist.details ? _refine_hist.d_res_high . _refine_hist.d_res_low . _refine_hist.number_atoms_solvent ? _refine_hist.number_atoms_total 2147 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand ? _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.019 0.014 2456 ? r_bond_refined_d ? ? 'ELECTRON MICROSCOPY' ? 1.004 0.020 978 ? r_bond_other_d ? ? 'ELECTRON MICROSCOPY' ? 0.898 1.289 3739 ? r_angle_refined_deg ? ? 'ELECTRON MICROSCOPY' ? 1.684 3.000 2389 ? r_angle_other_deg ? ? 'ELECTRON MICROSCOPY' ? 12.093 10.277 524 ? r_dihedral_angle_1_deg ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'ELECTRON MICROSCOPY' ? 0.161 0.214 424 ? r_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 1.004 0.020 1178 ? r_gen_planes_refined ? ? 'ELECTRON MICROSCOPY' ? 1.003 0.020 514 ? r_gen_planes_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_mcbond_it ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_mcbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_mcangle_it ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_mcangle_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scbond_it ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_it ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_long_range_B_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_long_range_B_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_rigid_bond_restr ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_free ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_ls_shell.d_res_high 6.500 _refine_ls_shell.d_res_low 6.668 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 22 _refine_ls_shell.number_reflns_R_work 319 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.816 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.736 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 7LJY _struct.title 'Cryo-EM structure of the B dENE construct complexed with a 28-mer poly(A)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7LJY _struct_keywords.text 'RNA triple helix, RNA stability, poly(A), SAXS and cryo-EM, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 7LJY 7LJY ? 1 ? 1 2 PDB 7LJY 7LJY ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7LJY B 1 ? 76 ? 7LJY 1 ? 76 ? 1 76 2 2 7LJY A 1 ? 28 ? 7LJY 1 ? 28 ? 1 28 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3730 ? 1 MORE -26 ? 1 'SSA (A^2)' 16750 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support SAXS _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 76 N3 ? ? B G 1 B C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 76 O2 ? ? B G 1 B C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 76 N4 ? ? B G 1 B C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 75 N3 ? ? B G 2 B C 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 75 O2 ? ? B G 2 B C 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 75 N4 ? ? B G 2 B C 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 74 N3 ? ? B G 3 B C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 74 O2 ? ? B G 3 B C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 74 N4 ? ? B G 3 B C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 N3 ? ? ? 1_555 A G 73 O6 ? ? B U 4 B G 73 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 73 N1 ? ? B U 4 B G 73 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 A A 68 N1 ? ? B C 6 B A 68 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 72 N1 ? ? B C 6 B G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 72 O6 ? ? B C 6 B G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 72 N2 ? ? B C 6 B G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 71 N1 ? ? B U 7 B A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 71 N6 ? ? B U 7 B A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 70 N1 ? ? B C 8 B G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 70 O6 ? ? B C 8 B G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 70 N2 ? ? B C 8 B G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 25 N1 ? ? B U 9 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 25 N6 ? ? B U 9 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 24 N1 ? ? B U 10 A A 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 24 N6 ? ? B U 10 A A 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 N3 ? ? ? 1_555 B A 23 N1 ? ? B U 11 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 11 O4 ? ? ? 1_555 B A 23 N6 ? ? B U 11 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 22 N1 ? ? B U 12 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 22 N6 ? ? B U 12 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 60 N1 ? ? B U 14 B A 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 60 N6 ? ? B U 14 B A 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 59 N1 ? ? B U 15 B A 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 15 O4 ? ? ? 1_555 A A 59 N6 ? ? B U 15 B A 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 58 N1 ? ? B U 16 B A 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 58 N6 ? ? B U 16 B A 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 17 N1 ? ? ? 1_555 A C 57 N3 ? ? B G 17 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N2 ? ? ? 1_555 A C 57 O2 ? ? B G 17 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 17 O6 ? ? ? 1_555 A C 57 N4 ? ? B G 17 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 18 N3 ? ? ? 1_555 A A 56 N1 ? ? B U 18 B A 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 18 O4 ? ? ? 1_555 A A 56 N6 ? ? B U 18 B A 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 19 N3 ? ? ? 1_555 A G 55 N1 ? ? B C 19 B G 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 19 N4 ? ? ? 1_555 A G 55 O6 ? ? B C 19 B G 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 19 O2 ? ? ? 1_555 A G 55 N2 ? ? B C 19 B G 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 20 N1 ? ? ? 1_555 A U 54 N3 ? ? B A 20 B U 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A A 20 N6 ? ? ? 1_555 A U 54 O4 ? ? B A 20 B U 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A U 21 N3 ? ? ? 1_555 A A 53 N1 ? ? B U 21 B A 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A U 21 O4 ? ? ? 1_555 A A 53 N6 ? ? B U 21 B A 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 22 N1 ? ? ? 1_555 A C 52 N3 ? ? B G 22 B C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 22 N2 ? ? ? 1_555 A C 52 O2 ? ? B G 22 B C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 22 O6 ? ? ? 1_555 A C 52 N4 ? ? B G 22 B C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 23 N1 ? ? ? 1_555 A A 51 N7 ? ? B G 23 B A 51 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog51 hydrog ? ? A G 23 O6 ? ? ? 1_555 A A 51 N6 ? ? B G 23 B A 51 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog52 hydrog ? ? A U 26 N3 ? ? ? 1_555 B A 8 N1 ? ? B U 26 A A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A U 26 O4 ? ? ? 1_555 B A 8 N6 ? ? B U 26 A A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A U 27 N3 ? ? ? 1_555 B A 7 N1 ? ? B U 27 A A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A U 27 O4 ? ? ? 1_555 B A 7 N6 ? ? B U 27 A A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 28 O2 ? ? ? 1_555 B A 6 N6 ? ? B C 28 A A 6 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog57 hydrog ? ? A C 28 N3 ? ? ? 1_555 A G 45 N1 ? ? B C 28 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 28 N4 ? ? ? 1_555 A G 45 O6 ? ? B C 28 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A C 28 O2 ? ? ? 1_555 A G 45 N2 ? ? B C 28 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A U 29 O2 ? ? ? 1_555 B A 4 N6 ? ? B U 29 A A 4 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog61 hydrog ? ? A U 29 N3 ? ? ? 1_555 A A 44 N1 ? ? B U 29 B A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A U 29 O4 ? ? ? 1_555 A A 44 N6 ? ? B U 29 B A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 30 O2 ? ? ? 1_555 B A 3 N6 ? ? B C 30 A A 3 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog64 hydrog ? ? A C 30 N3 ? ? ? 1_555 A G 43 N1 ? ? B C 30 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 30 N4 ? ? ? 1_555 A G 43 O6 ? ? B C 30 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 30 O2 ? ? ? 1_555 A G 43 N2 ? ? B C 30 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A A 31 N3 ? ? ? 1_555 B A 1 N6 ? ? B A 31 A A 1 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog68 hydrog ? ? A A 31 N1 ? ? ? 1_555 A U 42 N3 ? ? B A 31 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A A 31 N6 ? ? ? 1_555 A U 42 O4 ? ? B A 31 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A G 32 N1 ? ? ? 1_555 A C 41 N3 ? ? B G 32 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A G 32 N2 ? ? ? 1_555 A C 41 O2 ? ? B G 32 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A G 32 O6 ? ? ? 1_555 A C 41 N4 ? ? B G 32 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A G 33 N2 ? ? ? 1_555 A U 40 O2 ? ? B G 33 B U 40 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog74 hydrog ? ? A C 34 N3 ? ? ? 1_555 A G 39 N1 ? ? B C 34 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A C 34 N4 ? ? ? 1_555 A G 39 O6 ? ? B C 34 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A C 34 O2 ? ? ? 1_555 A G 39 N2 ? ? B C 34 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A G 35 N2 ? ? ? 1_555 A A 38 N7 ? ? B G 35 B A 38 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog78 hydrog ? ? A G 43 N2 ? ? ? 1_555 B A 2 N1 ? ? B G 43 A A 2 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog79 hydrog ? ? A G 43 N3 ? ? ? 1_555 B A 2 N6 ? ? B G 43 A A 2 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog80 hydrog ? ? A G 45 N2 ? ? ? 1_555 B A 5 N1 ? ? B G 45 A A 5 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog81 hydrog ? ? A G 45 N3 ? ? ? 1_555 B A 5 N6 ? ? B G 45 A A 5 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog82 hydrog ? ? A U 46 N3 ? ? ? 1_555 B A 6 N7 ? ? B U 46 A A 6 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog83 hydrog ? ? A U 46 O4 ? ? ? 1_555 B A 6 N6 ? ? B U 46 A A 6 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog84 hydrog ? ? A U 47 N3 ? ? ? 1_555 B A 7 N7 ? ? B U 47 A A 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog85 hydrog ? ? A U 47 O4 ? ? ? 1_555 B A 7 N6 ? ? B U 47 A A 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog86 hydrog ? ? A U 48 N3 ? ? ? 1_555 B A 8 N7 ? ? B U 48 A A 8 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog87 hydrog ? ? A U 49 N3 ? ? ? 1_555 B A 8 N7 ? ? B U 49 A A 8 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog88 hydrog ? ? A U 50 O2 ? ? ? 1_555 B A 9 N6 ? ? B U 50 A A 9 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog89 hydrog ? ? A U 62 N3 ? ? ? 1_555 B A 21 N7 ? ? B U 62 A A 21 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog90 hydrog ? ? A U 62 O4 ? ? ? 1_555 B A 21 N6 ? ? B U 62 A A 21 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog91 hydrog ? ? A U 63 N3 ? ? ? 1_555 B A 22 N7 ? ? B U 63 A A 22 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog92 hydrog ? ? A U 63 O4 ? ? ? 1_555 B A 22 N6 ? ? B U 63 A A 22 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog93 hydrog ? ? A U 64 N3 ? ? ? 1_555 B A 23 N7 ? ? B U 64 A A 23 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog94 hydrog ? ? A U 64 O4 ? ? ? 1_555 B A 23 N6 ? ? B U 64 A A 23 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog95 hydrog ? ? A U 65 N3 ? ? ? 1_555 B A 23 N7 ? ? B U 65 A A 23 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog96 hydrog ? ? A U 65 O4 ? ? ? 1_555 B A 23 N6 ? ? B U 65 A A 23 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog97 hydrog ? ? A U 65 N3 ? ? ? 1_555 B A 24 N7 ? ? B U 65 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog98 hydrog ? ? A U 65 O4 ? ? ? 1_555 B A 24 N6 ? ? B U 65 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog99 hydrog ? ? A U 66 N3 ? ? ? 1_555 B A 25 N7 ? ? B U 66 A A 25 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog100 hydrog ? ? A U 66 O4 ? ? ? 1_555 B A 25 N6 ? ? B U 66 A A 25 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _em_3d_fitting.entry_id 7LJY _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'RIGID BODY FIT' _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7LJY _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 283486 _em_3d_reconstruction.resolution 5.6 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'dENE construct complexed with a 28-mer poly(A)' _em_entity_assembly.source 'MULTIPLE SOURCES' _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list '1, 2' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7LJY _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type 'Quantifoil R2/1' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 100 _em_vitrification.instrument ? _em_vitrification.entry_id 7LJY _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7LJY _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 7LJY _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A A 26 ? B A 26 2 1 Y 1 A A 27 ? B A 27 3 1 Y 1 A A 28 ? B A 28 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.033 # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.ncbi_tax_id 4530 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Oryza sativa' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 50 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'PARTICLE SELECTION' ? EMAN2 2.3 1 ? ? 2 'IMAGE ACQUISITION' ? EPU 2.5 ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? CTFFIND 4.1 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? 'UCSF Chimera' ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 10 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 CLASSIFICATION ? cryoSPARC 2.15.0 1 ? ? 12 RECONSTRUCTION ? cryoSPARC 2.15.0 1 ? ? 13 'MODEL REFINEMENT' ? REFMAC ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7LJY 'double helix' 7LJY 'a-form double helix' 7LJY tetraloop 7LJY 'mismatched base pair' 7LJY 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 76 1_555 -0.406 -0.281 -0.119 13.461 -2.177 -2.543 1 B_G1:C76_B B 1 ? B 76 ? 19 1 1 A G 2 1_555 A C 75 1_555 -0.802 -0.578 -0.763 -0.009 -1.645 -0.721 2 B_G2:C75_B B 2 ? B 75 ? 19 1 1 A G 3 1_555 A C 74 1_555 -0.015 -0.186 -0.685 -13.980 -10.976 -0.886 3 B_G3:C74_B B 3 ? B 74 ? 19 1 1 A U 4 1_555 A G 73 1_555 2.027 -0.702 -0.918 -7.847 1.557 -6.832 4 B_U4:G73_B B 4 ? B 73 ? 28 1 1 A C 6 1_555 A G 72 1_555 -0.327 -0.197 -0.635 2.346 3.372 -1.384 5 B_C6:G72_B B 6 ? B 72 ? 19 1 1 A U 7 1_555 A A 71 1_555 -0.889 -0.136 -0.499 3.139 1.735 -11.254 6 B_U7:A71_B B 7 ? B 71 ? 20 1 1 A C 8 1_555 A G 70 1_555 0.750 -0.291 -0.435 17.468 -4.852 -6.344 7 B_C8:G70_B B 8 ? B 70 ? 19 1 1 A U 9 1_555 B A 25 1_555 0.506 -0.165 -0.318 14.719 -5.989 0.143 8 B_U9:A25_A B 9 ? A 25 ? 20 1 1 A U 10 1_555 B A 24 1_555 0.205 0.193 -0.406 27.060 -11.310 6.918 9 B_U10:A24_A B 10 ? A 24 ? 20 1 1 A U 11 1_555 B A 23 1_555 0.120 0.030 -0.735 28.864 -17.336 7.410 10 B_U11:A23_A B 11 ? A 23 ? 20 1 1 A U 12 1_555 B A 22 1_555 -0.495 -0.213 -0.701 -2.743 -3.603 4.303 11 B_U12:A22_A B 12 ? A 22 ? 20 1 1 A U 62 1_555 B A 21 1_555 -0.473 2.224 1.876 -26.317 -17.476 -83.491 12 B_U62:A21_A B 62 ? A 21 ? 23 3 1 A U 14 1_555 A A 60 1_555 -1.362 0.511 -0.655 39.799 -26.672 -24.234 13 B_U14:A60_B B 14 ? B 60 ? 20 1 1 A U 15 1_555 A A 59 1_555 -0.551 -0.242 -0.131 14.512 -28.659 -6.764 14 B_U15:A59_B B 15 ? B 59 ? 20 1 1 A U 16 1_555 A A 58 1_555 -1.035 -0.191 -0.448 13.847 -22.934 -4.702 15 B_U16:A58_B B 16 ? B 58 ? 20 1 1 A G 17 1_555 A C 57 1_555 -1.173 -0.543 0.328 4.341 -11.518 -1.870 16 B_G17:C57_B B 17 ? B 57 ? 19 1 1 A U 18 1_555 A A 56 1_555 -0.699 -0.250 -0.348 6.184 -18.927 -5.707 17 B_U18:A56_B B 18 ? B 56 ? 20 1 1 A C 19 1_555 A G 55 1_555 -0.512 -0.088 -0.112 6.297 -17.446 1.054 18 B_C19:G55_B B 19 ? B 55 ? 19 1 1 A A 20 1_555 A U 54 1_555 -0.021 -0.178 0.079 -0.851 -16.454 2.659 19 B_A20:U54_B B 20 ? B 54 ? 20 1 1 A U 21 1_555 A A 53 1_555 -0.491 -0.144 0.241 5.132 -21.709 -2.497 20 B_U21:A53_B B 21 ? B 53 ? 20 1 1 A G 22 1_555 A C 52 1_555 -0.483 -0.312 0.586 -13.727 -28.496 -5.491 21 B_G22:C52_B B 22 ? B 52 ? 19 1 1 A G 23 1_555 A A 51 1_555 -1.301 5.155 0.863 -19.432 -19.215 -111.782 22 B_G23:A51_B B 23 ? B 51 ? 9 3 1 B A 9 1_555 A U 50 1_555 -5.012 -0.707 -1.222 -22.523 2.094 -2.820 23 A_A9:U50_B A 9 ? B 50 ? ? ? 1 A U 26 1_555 B A 8 1_555 1.023 -0.412 0.640 -2.494 -7.031 -2.158 24 B_U26:A8_A B 26 ? A 8 ? 20 1 1 A U 27 1_555 B A 7 1_555 -0.225 -0.211 -0.611 2.266 -9.976 7.088 25 B_U27:A7_A B 27 ? A 7 ? 20 1 1 A C 28 1_555 A G 45 1_555 0.048 -0.113 0.236 22.042 -28.746 -3.143 26 B_C28:G45_B B 28 ? B 45 ? 19 1 1 A U 29 1_555 A A 44 1_555 0.130 -0.197 -0.301 2.275 -14.457 -0.110 27 B_U29:A44_B B 29 ? B 44 ? 20 1 1 A C 30 1_555 A G 43 1_555 0.262 -0.148 0.023 1.779 -11.564 4.345 28 B_C30:G43_B B 30 ? B 43 ? 19 1 1 A A 31 1_555 A U 42 1_555 0.084 -0.114 0.038 -2.202 -12.054 2.053 29 B_A31:U42_B B 31 ? B 42 ? 20 1 1 A G 32 1_555 A C 41 1_555 0.760 -0.149 0.159 -14.619 -6.794 -1.984 30 B_G32:C41_B B 32 ? B 41 ? 19 1 1 A G 33 1_555 A U 40 1_555 0.783 -0.243 0.897 5.300 -23.548 -11.349 31 B_G33:U40_B B 33 ? B 40 ? ? 1 1 A C 34 1_555 A G 39 1_555 0.489 -0.308 -0.080 12.620 -8.659 -6.541 32 B_C34:G39_B B 34 ? B 39 ? 19 1 1 A G 35 1_555 A A 38 1_555 7.422 -4.132 1.072 28.323 3.065 -38.911 33 B_G35:A38_B B 35 ? B 38 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 76 1_555 A G 2 1_555 A C 75 1_555 -0.010 -1.933 4.456 -3.480 -5.113 29.589 -2.242 -0.978 4.687 -9.875 6.722 30.214 1 BB_G1G2:C75C76_BB B 1 ? B 76 ? B 2 ? B 75 ? 1 A G 2 1_555 A C 75 1_555 A G 3 1_555 A C 74 1_555 0.500 -2.034 3.812 4.079 12.090 35.238 -4.886 -0.202 3.015 19.211 -6.481 37.408 2 BB_G2G3:C74C75_BB B 2 ? B 75 ? B 3 ? B 74 ? 1 A G 3 1_555 A C 74 1_555 A U 4 1_555 A G 73 1_555 -0.171 -1.673 3.194 3.038 -2.996 41.360 -2.042 0.560 3.282 -4.229 -4.288 41.570 3 BB_G3U4:G73C74_BB B 3 ? B 74 ? B 4 ? B 73 ? 1 A U 4 1_555 A G 73 1_555 A C 6 1_555 A G 72 1_555 -2.491 -1.565 3.368 9.792 6.913 43.527 -2.611 4.056 2.515 9.118 -12.916 45.070 4 BB_U4C6:G72G73_BB B 4 ? B 73 ? B 6 ? B 72 ? 1 A C 6 1_555 A G 72 1_555 A U 7 1_555 A A 71 1_555 -0.487 -2.038 3.446 2.834 3.783 28.687 -4.897 1.597 3.096 7.569 -5.672 29.066 5 BB_C6U7:A71G72_BB B 6 ? B 72 ? B 7 ? B 71 ? 1 A U 7 1_555 A A 71 1_555 A C 8 1_555 A G 70 1_555 0.496 -1.437 3.078 -0.124 4.123 36.833 -2.768 -0.795 2.904 6.500 0.196 37.055 6 BB_U7C8:G70A71_BB B 7 ? B 71 ? B 8 ? B 70 ? 1 A C 8 1_555 A G 70 1_555 A U 9 1_555 B A 25 1_555 1.478 -2.290 3.550 2.128 2.500 37.189 -3.933 -2.007 3.470 3.910 -3.328 37.329 7 BB_C8U9:A25G70_AB B 8 ? B 70 ? B 9 ? A 25 ? 1 A U 9 1_555 B A 25 1_555 A U 10 1_555 B A 24 1_555 0.475 -1.787 3.298 -2.193 6.384 29.415 -4.664 -1.336 2.814 12.367 4.248 30.163 8 BB_U9U10:A24A25_AA B 9 ? A 25 ? B 10 ? A 24 ? 1 A U 10 1_555 B A 24 1_555 A U 11 1_555 B A 23 1_555 -0.292 -1.720 3.527 0.966 5.362 26.739 -5.020 0.867 3.116 11.444 -2.061 27.279 9 BB_U10U11:A23A24_AA B 10 ? A 24 ? B 11 ? A 23 ? 1 A U 11 1_555 B A 23 1_555 A U 12 1_555 B A 22 1_555 -0.153 -2.472 4.233 -6.015 12.761 24.225 -8.510 -1.285 2.596 27.614 13.016 27.981 10 BB_U11U12:A22A23_AA B 11 ? A 23 ? B 12 ? A 22 ? 1 A U 12 1_555 B A 22 1_555 A U 62 1_555 B A 21 1_555 -0.114 4.040 2.479 144.270 86.209 -62.541 -2.329 0.447 -0.393 -44.573 74.591 -169.804 11 BB_U12U62:A21A22_AA B 12 ? A 22 ? B 62 ? A 21 ? 1 A U 14 1_555 A A 60 1_555 A U 15 1_555 A A 59 1_555 0.906 -1.570 3.939 -3.459 5.709 41.827 -2.852 -1.665 3.621 7.935 4.809 42.333 12 BB_U14U15:A59A60_BB B 14 ? B 60 ? B 15 ? B 59 ? 1 A U 15 1_555 A A 59 1_555 A U 16 1_555 A A 58 1_555 -0.215 -1.077 3.264 -0.512 9.956 28.716 -3.948 0.313 2.749 19.351 0.994 30.363 13 BB_U15U16:A58A59_BB B 15 ? B 59 ? B 16 ? B 58 ? 1 A U 16 1_555 A A 58 1_555 A G 17 1_555 A C 57 1_555 0.727 -1.593 3.312 -7.580 15.780 30.488 -4.729 -2.208 2.038 27.359 13.143 35.052 14 BB_U16G17:C57A58_BB B 16 ? B 58 ? B 17 ? B 57 ? 1 A G 17 1_555 A C 57 1_555 A U 18 1_555 A A 56 1_555 -0.864 -1.450 3.086 0.539 5.067 37.220 -2.856 1.406 2.858 7.894 -0.840 37.555 15 BB_G17U18:A56C57_BB B 17 ? B 57 ? B 18 ? B 56 ? 1 A U 18 1_555 A A 56 1_555 A C 19 1_555 A G 55 1_555 0.826 -1.193 3.221 0.130 7.945 33.696 -3.164 -1.370 2.876 13.473 -0.220 34.594 16 BB_U18C19:G55A56_BB B 18 ? B 56 ? B 19 ? B 55 ? 1 A C 19 1_555 A G 55 1_555 A A 20 1_555 A U 54 1_555 0.410 -1.548 3.225 -0.226 19.014 32.386 -4.580 -0.665 2.036 30.985 0.369 37.426 17 BB_C19A20:U54G55_BB B 19 ? B 55 ? B 20 ? B 54 ? 1 A A 20 1_555 A U 54 1_555 A U 21 1_555 A A 53 1_555 0.127 -1.733 3.043 -0.430 -2.629 30.427 -2.793 -0.323 3.176 -4.998 0.818 30.541 18 BB_A20U21:A53U54_BB B 20 ? B 54 ? B 21 ? B 53 ? 1 A U 21 1_555 A A 53 1_555 A G 22 1_555 A C 52 1_555 -0.419 -1.644 3.610 -3.747 5.610 36.858 -3.351 0.125 3.357 8.783 5.866 37.449 19 BB_U21G22:C52A53_BB B 21 ? B 53 ? B 22 ? B 52 ? 1 A G 22 1_555 A C 52 1_555 A G 23 1_555 A A 51 1_555 -0.284 -2.125 2.491 0.376 0.365 68.837 -1.890 0.262 2.480 0.323 -0.332 68.839 20 BB_G22G23:A51C52_BB B 22 ? B 52 ? B 23 ? B 51 ? 1 A G 23 1_555 A A 51 1_555 B A 9 1_555 A U 50 1_555 -2.591 -5.452 0.521 -158.242 -3.768 100.250 -2.735 0.828 2.129 -1.943 81.604 166.129 21 BA_G23A9:U50A51_BB B 23 ? B 51 ? A 9 ? B 50 ? 1 B A 9 1_555 A U 50 1_555 A U 26 1_555 B A 8 1_555 -2.781 -3.774 -1.752 160.883 -36.170 -13.755 1.894 -1.443 1.660 19.542 86.921 -165.008 22 AB_A9U26:A8U50_AB A 9 ? B 50 ? B 26 ? A 8 ? 1 A U 26 1_555 B A 8 1_555 A U 27 1_555 B A 7 1_555 0.702 -2.200 3.193 6.910 -0.248 24.494 -4.924 0.410 3.285 -0.570 -15.886 25.437 23 BB_U26U27:A7A8_AA B 26 ? A 8 ? B 27 ? A 7 ? 1 A U 27 1_555 B A 7 1_555 A C 28 1_555 A G 45 1_555 5.681 -0.404 3.221 -13.660 0.913 83.474 -0.319 -4.509 2.438 0.682 10.199 84.386 24 BB_U27C28:G45A7_BA B 27 ? A 7 ? B 28 ? B 45 ? 1 A U 29 1_555 A A 44 1_555 A C 30 1_555 A G 43 1_555 0.373 -1.427 3.189 -0.330 9.380 32.062 -3.909 -0.699 2.673 16.544 0.582 33.373 25 BB_U29C30:G43A44_BB B 29 ? B 44 ? B 30 ? B 43 ? 1 A C 30 1_555 A G 43 1_555 A A 31 1_555 A U 42 1_555 -0.411 -1.324 3.161 -0.297 9.555 33.002 -3.610 0.654 2.688 16.396 0.509 34.322 26 BB_C30A31:U42G43_BB B 30 ? B 43 ? B 31 ? B 42 ? 1 A A 31 1_555 A U 42 1_555 A G 32 1_555 A C 41 1_555 -0.391 -1.200 4.192 -1.833 8.782 34.468 -3.553 0.308 3.797 14.518 3.031 35.582 27 BB_A31G32:C41U42_BB B 31 ? B 42 ? B 32 ? B 41 ? 1 A G 32 1_555 A C 41 1_555 A G 33 1_555 A U 40 1_555 -0.542 -2.058 2.773 -7.146 15.813 30.036 -5.220 0.117 1.607 27.789 12.558 34.588 28 BB_G32G33:U40C41_BB B 32 ? B 41 ? B 33 ? B 40 ? 1 A G 33 1_555 A U 40 1_555 A C 34 1_555 A G 39 1_555 -0.423 -1.895 3.348 -0.436 1.209 31.719 -3.690 0.693 3.281 2.211 0.798 31.744 29 BB_G33C34:G39U40_BB B 33 ? B 40 ? B 34 ? B 39 ? 1 A C 34 1_555 A G 39 1_555 A G 35 1_555 A A 38 1_555 -3.541 -2.303 3.045 -0.061 15.477 48.331 -3.604 4.139 2.259 18.364 0.073 50.607 30 BB_C34G35:A38G39_BB B 34 ? B 39 ? B 35 ? B 38 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' P41GM103832 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' P01AI120943 2 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' S10OD021600 3 # _atom_sites.entry_id 7LJY _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O P # loop_