data_8UPY # _entry.id 8UPY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8UPY pdb_00008upy 10.2210/pdb8upy/pdb WWPDB D_1000278556 ? ? EMDB EMD-42457 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2024-09-04 # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8UPY _pdbx_database_status.recvd_initial_deposition_date 2023-10-23 _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 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Methanosarcine mazei tRNAPyl in A-site of ribosome' _pdbx_database_related.db_id EMD-42457 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 3 _pdbx_contact_author.email dieter.soll@yale.edu _pdbx_contact_author.name_first Dieter _pdbx_contact_author.name_last Soll _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-3077-8986 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Krahn, N.' 1 0000-0003-0696-433X 'Zhang, J.' 2 ? 'Melnikov, S.V.' 3 ? 'Tharp, J.M.' 4 0000-0002-2362-3249 'Villa, A.' 5 ? 'Patel, A.' 6 ? 'Howard, R.J.' 7 0000-0003-2049-3378 'Gabir, H.' 8 ? 'Patel, T.R.' 9 0000-0003-0627-2923 'Stetefeld, J.' 10 0000-0003-1478-3248 'Puglisi, J.' 11 ? 'Soll, D.' 12 0000-0002-3077-8986 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 513 _citation.page_last 524 _citation.title 'tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkad1188 _citation.pdbx_database_id_PubMed 38100361 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Krahn, N.' 1 0000-0003-0696-433X primary 'Zhang, J.' 2 ? primary 'Melnikov, S.V.' 3 ? primary 'Tharp, J.M.' 4 ? primary 'Villa, A.' 5 ? primary 'Patel, A.' 6 ? primary 'Howard, R.J.' 7 ? primary 'Gabir, H.' 8 ? primary 'Patel, T.R.' 9 0000-0003-0627-2923 primary 'Stetefeld, J.' 10 ? primary 'Puglisi, J.' 11 0000-0001-9268-5112 primary 'Soll, D.' 12 0000-0002-3077-8986 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'RNA (72-MER)' _entity.formula_weight 23114.709 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGAAACCUGAUCAUGUAGAUCGAAUGGACUCUAAAUCCGUUCAGCCGGGUUAGAUUCCCGGGGUUUCCGCCA _entity_poly.pdbx_seq_one_letter_code_can GGAAACCUGAUCAUGUAGAUCGAAUGGACUCUAAAUCCGUUCAGCCGGGUUAGAUUCCCGGGGUUUCCGCCA _entity_poly.pdbx_strand_id C _entity_poly.pdbx_target_identifier ? # 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 A n 1 4 A n 1 5 A n 1 6 C n 1 7 C n 1 8 U n 1 9 G n 1 10 A n 1 11 U n 1 12 C n 1 13 A n 1 14 U n 1 15 G n 1 16 U n 1 17 A n 1 18 G n 1 19 A n 1 20 U n 1 21 C n 1 22 G n 1 23 A n 1 24 A n 1 25 U n 1 26 G n 1 27 G n 1 28 A n 1 29 C n 1 30 U n 1 31 C n 1 32 U n 1 33 A n 1 34 A n 1 35 A n 1 36 U n 1 37 C n 1 38 C n 1 39 G n 1 40 U n 1 41 U n 1 42 C n 1 43 A n 1 44 G n 1 45 C n 1 46 C n 1 47 G n 1 48 G n 1 49 G n 1 50 U n 1 51 U n 1 52 A n 1 53 G n 1 54 A n 1 55 U n 1 56 U n 1 57 C n 1 58 C n 1 59 C n 1 60 G n 1 61 G n 1 62 G n 1 63 G n 1 64 U n 1 65 U n 1 66 U n 1 67 C n 1 68 C n 1 69 G n 1 70 C n 1 71 C n 1 72 A n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 72 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene pylT _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Methanosarcina mazei' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2209 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'in vitro transcription vector pT7-TP(deltai)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 905931 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 C . n A 1 2 G 2 2 2 G G C . n A 1 3 A 3 3 3 A A C . n A 1 4 A 4 4 4 A A C . n A 1 5 A 5 5 5 A A C . n A 1 6 C 6 6 6 C C C . n A 1 7 C 7 7 7 C C C . n A 1 8 U 8 8 8 U U C . n A 1 9 G 9 10 10 G G C . n A 1 10 A 10 11 11 A A C . n A 1 11 U 11 12 12 U U C . n A 1 12 C 12 13 13 C C C . n A 1 13 A 13 14 14 A A C . n A 1 14 U 14 15 15 U U C . n A 1 15 G 15 18 18 G G C . n A 1 16 U 16 19 19 U U C . n A 1 17 A 17 20 20 A A C . n A 1 18 G 18 21 21 G G C . n A 1 19 A 19 22 22 A A C . n A 1 20 U 20 23 23 U U C . n A 1 21 C 21 24 24 C C C . n A 1 22 G 22 25 25 G G C . n A 1 23 A 23 26 26 A A C . n A 1 24 A 24 27 27 A A C . n A 1 25 U 25 28 28 U U C . n A 1 26 G 26 29 29 G G C . n A 1 27 G 27 30 30 G G C . n A 1 28 A 28 31 31 A A C . n A 1 29 C 29 32 32 C C C . n A 1 30 U 30 33 33 U U C . n A 1 31 C 31 34 34 C C C . n A 1 32 U 32 35 35 U U C . n A 1 33 A 33 36 36 A A C . n A 1 34 A 34 37 37 A A C . n A 1 35 A 35 38 38 A A C . n A 1 36 U 36 39 39 U U C . n A 1 37 C 37 40 40 C C C . n A 1 38 C 38 41 41 C C C . n A 1 39 G 39 42 42 G G C . n A 1 40 U 40 43 43 U U C . n A 1 41 U 41 44 44 U U C . n A 1 42 C 42 45 45 C C C . n A 1 43 A 43 47 47 A A C . n A 1 44 G 44 48 48 G G C . n A 1 45 C 45 49 49 C C C . n A 1 46 C 46 50 50 C C C . n A 1 47 G 47 51 51 G G C . n A 1 48 G 48 52 52 G G C . n A 1 49 G 49 53 53 G G C . n A 1 50 U 50 54 54 U U C . n A 1 51 U 51 55 55 U U C . n A 1 52 A 52 56 56 A A C . n A 1 53 G 53 57 57 G G C . n A 1 54 A 54 58 58 A A C . n A 1 55 U 55 59 59 U U C . n A 1 56 U 56 60 60 U U C . n A 1 57 C 57 61 61 C C C . n A 1 58 C 58 62 62 C C C . n A 1 59 C 59 63 63 C C C . n A 1 60 G 60 64 64 G G C . n A 1 61 G 61 65 65 G G C . n A 1 62 G 62 66 66 G G C . n A 1 63 G 63 67 67 G G C . n A 1 64 U 64 68 68 U U C . n A 1 65 U 65 69 69 U U C . n A 1 66 U 66 70 70 U U C . n A 1 67 C 67 71 71 C C C . n A 1 68 C 68 72 72 C C C . n A 1 69 G 69 73 73 G G C . n A 1 70 C 70 74 74 C C C . n A 1 71 C 71 75 75 C C C . n A 1 72 A 72 76 76 A A C . n # _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 8UPY _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 8UPY _struct.title 'Methanosarcine mazei tRNAPyl in A-site of ribosome' _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 8UPY _struct_keywords.text 'tRNA, pyrrolysine, translation, RNA' _struct_keywords.pdbx_keywords RNA # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code AP019780.1 _struct_ref.pdbx_db_accession 2047643091 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GGAAACCUGAUCAUGUAGAUCGAAUGGACUCUAAAUCCGUUCAGCCGGGUUAGAUUCCCGGGGUUUCCGCCA _struct_ref.pdbx_align_begin 3434586 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8UPY _struct_ref_seq.pdbx_strand_id C _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 72 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2047643091 _struct_ref_seq.db_align_beg 3434586 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 3434657 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 76 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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 x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # 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 68 N3 ? ? C G 1 C C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 68 O2 ? ? C G 1 C C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 68 N4 ? ? C G 1 C C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 67 N3 ? ? C G 2 C C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 67 O2 ? ? C G 2 C C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 67 N4 ? ? C G 2 C C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A C 67 N4 ? ? C A 3 C C 71 1_555 ? ? ? ? ? ? TYPE_26_PAIR ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A C 67 N3 ? ? C A 3 C C 71 1_555 ? ? ? ? ? ? TYPE_26_PAIR ? ? ? hydrog9 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 65 N3 ? ? C A 4 C U 69 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 66 N3 ? ? C A 4 C U 70 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 64 N3 ? ? C A 5 C U 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 64 O4 ? ? C A 5 C U 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 63 N1 ? ? C C 6 C G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 63 O6 ? ? C C 6 C G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 63 N2 ? ? C C 6 C G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 62 N2 ? ? C C 7 C G 66 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog17 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 62 N1 ? ? C C 7 C G 66 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog18 hydrog ? ? A U 8 N3 ? ? ? 1_555 A U 11 O4 ? ? C U 8 C U 12 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog19 hydrog ? ? A U 8 O4 ? ? ? 1_555 A U 11 N3 ? ? C U 8 C U 12 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog20 hydrog ? ? A U 8 O2 ? ? ? 1_555 A G 18 N2 ? ? C U 8 C G 21 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog21 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 20 N3 ? ? C A 11 C U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 20 O4 ? ? C A 11 C U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 19 N6 ? ? C U 12 C A 22 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog24 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 18 N3 ? ? C C 13 C G 21 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog25 hydrog ? ? A A 13 N6 ? ? ? 1_555 A G 44 N7 ? ? C A 14 C G 48 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog26 hydrog ? ? A G 15 N1 ? ? ? 1_555 A U 51 O2 ? ? C G 18 C U 55 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog27 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 52 N1 ? ? C U 19 C A 56 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog28 hydrog ? ? A A 19 N6 ? ? ? 1_555 A A 43 N1 ? ? C A 22 C A 47 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog29 hydrog ? ? A A 19 N7 ? ? ? 1_555 A A 43 N6 ? ? C A 22 C A 47 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog30 hydrog ? ? A A 24 N1 ? ? ? 1_555 A U 40 N3 ? ? C A 27 C U 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 24 N6 ? ? ? 1_555 A U 40 O4 ? ? C A 27 C U 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 25 N3 ? ? ? 1_555 A U 40 O4 ? ? C U 28 C U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog33 hydrog ? ? A U 25 O2 ? ? ? 1_555 A U 40 N3 ? ? C U 28 C U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog34 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 38 N3 ? ? C G 29 C C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 38 O2 ? ? C G 29 C C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 38 N4 ? ? C G 29 C C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 27 N1 ? ? ? 1_555 A C 37 N3 ? ? C G 30 C C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 27 N2 ? ? ? 1_555 A C 37 O2 ? ? C G 30 C C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 27 O6 ? ? ? 1_555 A C 37 N4 ? ? C G 30 C C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A A 28 N1 ? ? ? 1_555 A A 35 N6 ? ? C A 31 C A 38 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog41 hydrog ? ? A C 29 O2 ? ? ? 1_555 A A 35 N6 ? ? C C 32 C A 38 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog42 hydrog ? ? A C 45 N3 ? ? ? 1_555 A G 61 N2 ? ? C C 49 C G 65 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog43 hydrog ? ? A C 45 O2 ? ? ? 1_555 A G 61 N1 ? ? C C 49 C G 65 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog44 hydrog ? ? A C 46 N3 ? ? ? 1_555 A G 60 N1 ? ? C C 50 C G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 46 N4 ? ? ? 1_555 A G 60 O6 ? ? C C 50 C G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 46 O2 ? ? ? 1_555 A G 60 N2 ? ? C C 50 C G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 47 N1 ? ? ? 1_555 A C 59 N3 ? ? C G 51 C C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 47 N2 ? ? ? 1_555 A C 59 O2 ? ? C G 51 C C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 47 O6 ? ? ? 1_555 A C 59 N4 ? ? C G 51 C C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 48 N2 ? ? ? 1_555 A C 58 O2 ? ? C G 52 C C 62 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog51 hydrog ? ? A G 49 N1 ? ? ? 1_555 A C 57 N3 ? ? C G 53 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 49 N2 ? ? ? 1_555 A C 57 O2 ? ? C G 53 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 49 O6 ? ? ? 1_555 A C 57 N4 ? ? C G 53 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N4 C C 49 ? ? O6 C G 65 ? ? 1.04 2 1 N3 C C 49 ? ? N1 C G 65 ? ? 1.33 3 1 N4 C C 7 ? ? O6 C G 66 ? ? 1.56 4 1 O2 C C 49 ? ? N2 C G 65 ? ? 1.58 5 1 N3 C C 7 ? ? N1 C G 66 ? ? 1.82 6 1 N4 C C 49 ? ? C6 C G 65 ? ? 1.84 7 1 N3 C G 51 ? ? N2 C G 64 ? ? 1.87 8 1 C4 C G 51 ? ? N2 C G 64 ? ? 1.90 9 1 C6 C G 1 ? ? N1 C G 73 ? ? 1.91 10 1 N1 C A 14 ? ? N7 C G 48 ? ? 1.97 11 1 O2 C C 7 ? ? N2 C G 66 ? ? 1.99 12 1 C4 C G 1 ? ? N2 C G 73 ? ? 2.01 13 1 O6 C G 1 ? ? C6 C G 73 ? ? 2.05 14 1 C4 C C 49 ? ? O6 C G 65 ? ? 2.07 15 1 N2 C G 51 ? ? N3 C G 64 ? ? 2.07 16 1 O6 C G 1 ? ? O6 C G 73 ? ? 2.09 17 1 N3 C U 12 ? ? N1 C A 22 ? ? 2.10 18 1 C2 C G 1 ? ? N3 C G 73 ? ? 2.10 19 1 N6 C A 26 ? ? O4 C U 44 ? ? 2.11 20 1 C2 C G 51 ? ? C2 C G 64 ? ? 2.12 21 1 N1 C A 3 ? ? N3 C C 71 ? ? 2.13 22 1 C2 C G 51 ? ? N3 C G 64 ? ? 2.16 23 1 C4 C C 49 ? ? N1 C G 65 ? ? 2.16 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" C G 51 ? ? "O3'" C G 51 ? ? P C G 52 ? ? 111.22 119.70 -8.48 1.20 Y 2 1 "O3'" C G 51 ? ? P C G 52 ? ? "O5'" C G 52 ? ? 91.14 104.00 -12.86 1.90 Y 3 1 "C3'" C U 60 ? ? "O3'" C U 60 ? ? P C C 61 ? ? 126.95 119.70 7.25 1.20 Y # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8UPY _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 8UPY _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.8 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 405164 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.4 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Complex of tRNAPyl in the A-site of the E. coli ribosome' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 8UPY _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 8UPY _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE-PROPANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details 'blot for 3 seconds before plunging' # _em_experiment.entry_id 8UPY _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state '3D ARRAY' _em_experiment.entity_assembly_id 1 # 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_admin.current_status REL _em_admin.deposition_date 2023-10-23 _em_admin.deposition_site RCSB _em_admin.entry_id 8UPY _em_admin.last_update 2024-09-04 _em_admin.map_release_date 2024-09-04 _em_admin.title 'Methanosarcine mazei tRNAPyl in A-site of ribosome' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 2209 _em_entity_assembly_naturalsource.organism 'Methanosarcina mazei' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 905931 _em_entity_assembly_recombinant.organism 'in vitro transcription vector pT7-TP(deltai)' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 40 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? CTFFIND 4 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _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 8UPY 'double helix' 8UPY 'a-form double helix' 8UPY 'parallel strands' 8UPY 'hairpin loop' 8UPY 'bulge loop' 8UPY 'mismatched base pair' 8UPY 'quadruple helix' # 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 68 1_555 -1.531 -0.685 -0.976 2.258 -13.463 17.449 1 C_G1:C72_C C 1 ? C 72 ? 19 1 1 A G 2 1_555 A C 67 1_555 -1.533 -1.090 -1.012 -3.704 7.424 -1.068 2 C_G2:C71_C C 2 ? C 71 ? 19 1 1 A A 4 1_555 A U 65 1_555 -1.141 0.872 -0.481 -4.676 -28.539 28.158 3 C_A4:U69_C C 4 ? C 69 ? ? 1 1 A A 5 1_555 A U 64 1_555 -1.499 -0.616 -0.870 -3.296 -8.966 2.254 4 C_A5:U68_C C 5 ? C 68 ? 20 1 1 A C 6 1_555 A G 63 1_555 1.245 -0.668 -0.433 -2.350 -13.604 -0.329 5 C_C6:G67_C C 6 ? C 67 ? 19 1 1 A C 7 1_555 A G 62 1_555 -0.168 -1.265 0.190 6.040 -6.765 -7.919 6 C_C7:G66_C C 7 ? C 66 ? 22 1 1 A C 45 1_555 A G 61 1_555 -0.443 -1.870 0.534 2.758 -4.358 -11.721 7 C_C49:G65_C C 49 ? C 65 ? 22 1 1 A C 46 1_555 A G 60 1_555 1.500 -0.630 -1.103 3.470 -35.909 17.023 8 C_C50:G64_C C 50 ? C 64 ? 19 1 1 A G 47 1_555 A C 59 1_555 1.065 0.401 -0.518 9.769 -11.062 -0.202 9 C_G51:C63_C C 51 ? C 63 ? 19 1 1 A G 48 1_555 A C 58 1_555 0.204 0.501 -1.155 -10.623 -4.399 18.720 10 C_G52:C62_C C 52 ? C 62 ? ? 1 1 A G 49 1_555 A C 57 1_555 1.321 0.129 -0.619 -18.766 -25.184 7.722 11 C_G53:C61_C C 53 ? C 61 ? 19 1 1 A U 51 1_555 A G 15 1_555 0.675 -5.177 -0.628 24.515 -2.658 -100.328 12 C_U55:G18_C C 55 ? C 18 ? ? 6 1 A A 10 1_555 A U 20 1_555 -0.549 -0.587 -0.171 -6.073 -19.738 -6.368 13 C_A11:U23_C C 11 ? C 23 ? 20 1 1 A U 11 1_555 A A 19 1_555 -0.178 -0.676 0.708 -0.161 -17.087 21.472 14 C_U12:A22_C C 12 ? C 22 ? ? 1 1 A C 12 1_555 A G 18 1_555 -6.952 -3.287 -0.271 6.750 -0.446 50.008 15 C_C13:G21_C C 13 ? C 21 ? ? 5 1 A A 13 1_555 A G 44 1_555 5.433 -1.228 -0.109 11.631 -4.127 -116.048 16 C_A14:G48_C C 14 ? C 48 ? ? 4 1 A U 16 1_555 A A 52 1_555 -1.682 0.145 0.983 -24.532 -27.476 10.855 17 C_U19:A56_C C 19 ? C 56 ? ? ? 1 A A 24 1_555 A U 40 1_555 1.050 0.025 -0.885 3.605 -18.561 -17.405 18 C_A27:U43_C C 27 ? C 43 ? 20 1 1 A G 26 1_555 A C 38 1_555 0.298 -0.137 -0.557 0.316 -16.614 -8.424 19 C_G29:C41_C C 29 ? C 41 ? 19 1 1 A G 27 1_555 A C 37 1_555 0.025 -0.207 0.286 -5.275 -3.614 -7.771 20 C_G30:C40_C C 30 ? C 40 ? 19 1 1 A A 28 1_555 A A 35 1_555 4.128 1.154 -1.885 -20.252 -15.472 -39.131 21 C_A31:A38_C C 31 ? C 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 68 1_555 A G 2 1_555 A C 67 1_555 -0.879 -0.452 3.630 -7.437 1.750 41.806 -0.824 0.360 3.706 2.428 10.318 42.468 1 CC_G1G2:C71C72_CC C 1 ? C 72 ? C 2 ? C 71 ? 1 A G 2 1_555 A C 67 1_555 A A 4 1_555 A U 65 1_555 0.992 -2.936 6.280 2.167 14.896 58.480 -4.265 -0.793 5.485 14.978 -2.179 60.221 2 CC_G2A4:U69C71_CC C 2 ? C 71 ? C 4 ? C 69 ? 1 A A 4 1_555 A U 65 1_555 A A 5 1_555 A U 64 1_555 -0.885 -1.312 3.305 -8.172 8.885 26.285 -4.585 -0.023 2.864 18.357 16.882 28.880 3 CC_A4A5:U68U69_CC C 4 ? C 69 ? C 5 ? C 68 ? 1 A A 5 1_555 A U 64 1_555 A C 6 1_555 A G 63 1_555 0.384 -1.026 3.474 0.470 -1.181 53.035 -1.068 -0.398 3.498 -1.322 -0.526 53.049 4 CC_A5C6:G67U68_CC C 5 ? C 68 ? C 6 ? C 67 ? 1 A C 6 1_555 A G 63 1_555 A C 7 1_555 A G 62 1_555 -0.752 -1.372 2.495 6.499 19.423 13.243 -6.380 2.830 0.075 54.482 -18.230 24.351 5 CC_C6C7:G66G67_CC C 6 ? C 67 ? C 7 ? C 66 ? 1 A C 7 1_555 A G 62 1_555 A C 45 1_555 A G 61 1_555 -0.055 -2.775 3.311 -5.758 10.919 36.331 -5.457 -0.563 2.390 16.922 8.924 38.304 6 CC_C7C49:G65G66_CC C 7 ? C 66 ? C 49 ? C 65 ? 1 A C 45 1_555 A G 61 1_555 A C 46 1_555 A G 60 1_555 -0.044 -0.253 3.213 15.764 18.418 47.069 -1.462 1.057 2.798 21.481 -18.386 52.628 7 CC_C49C50:G64G65_CC C 49 ? C 65 ? C 50 ? C 64 ? 1 A C 46 1_555 A G 60 1_555 A G 47 1_555 A C 59 1_555 -1.569 -1.194 3.409 -10.920 8.252 26.155 -4.262 0.552 3.277 16.845 22.293 29.465 8 CC_C50G51:C63G64_CC C 50 ? C 64 ? C 51 ? C 63 ? 1 A G 47 1_555 A C 59 1_555 A G 48 1_555 A C 58 1_555 0.396 -1.756 3.811 -2.004 11.690 24.842 -6.701 -1.348 2.687 25.406 4.355 27.487 9 CC_G51G52:C62C63_CC C 51 ? C 63 ? C 52 ? C 62 ? 1 A G 48 1_555 A C 58 1_555 A G 49 1_555 A C 57 1_555 -0.320 -1.176 4.038 3.475 0.203 37.954 -1.833 1.030 3.988 0.312 -5.329 38.107 10 CC_G52G53:C61C62_CC C 52 ? C 62 ? C 53 ? C 61 ? 1 A G 49 1_555 A C 57 1_555 A U 51 1_555 A G 15 1_555 -0.360 -0.706 5.920 9.545 8.137 118.859 -0.552 0.376 5.860 4.719 -5.535 119.264 11 CC_G53U55:G18C61_CC C 53 ? C 61 ? C 55 ? C 18 ? 1 A A 10 1_555 A U 20 1_555 A U 11 1_555 A A 19 1_555 1.896 -0.946 3.136 -5.714 5.561 25.833 -3.253 -5.320 2.416 12.078 12.410 27.015 12 CC_A11U12:A22U23_CC C 11 ? C 23 ? C 12 ? C 22 ? 1 A U 11 1_555 A A 19 1_555 A C 12 1_555 A G 18 1_555 3.701 -4.232 2.844 2.693 1.233 -10.337 20.987 23.245 2.294 -6.665 14.561 -10.752 13 CC_U12C13:G21A22_CC C 12 ? C 22 ? C 13 ? C 21 ? 1 A C 12 1_555 A G 18 1_555 A A 13 1_555 A G 44 1_555 0.663 -0.457 3.426 1.024 7.369 151.090 -0.265 -0.338 3.419 3.805 -0.529 151.152 14 CC_C13A14:G48G21_CC C 13 ? C 21 ? C 14 ? C 48 ? 1 A G 26 1_555 A C 38 1_555 A G 27 1_555 A C 37 1_555 0.489 -2.554 3.168 -1.903 15.668 37.247 -5.147 -0.884 1.955 23.291 2.829 40.344 15 CC_G29G30:C40C41_CC C 29 ? C 41 ? C 30 ? C 40 ? 1 A G 27 1_555 A C 37 1_555 A A 28 1_555 A A 35 1_555 -1.210 -2.743 4.764 -0.081 17.311 59.781 -3.747 1.169 3.915 16.986 0.080 62.014 16 CC_G30A31:A38C40_CC C 30 ? C 40 ? C 31 ? C 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' 'R35 GM122560' 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'R35 GM122560-05S1' 2 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM51266 3 'Department of Energy (DOE, United States)' 'United States' DE-FG0298ER2031 4 'Cystic Fibrosis Foundation' 'United States' PUGLIS20G0 5 'Knut and Alice Wallenberg Foundation' Sweden 'KAW 2016.0488' 6 # _atom_sites.entry_id 8UPY _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.Cartn_transform_axes ? _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_