data_8DST # _entry.id 8DST # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 8DST pdb_00008dst 10.2210/pdb8dst/pdb WWPDB D_1000267304 ? ? EMDB EMD-27688 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM of NBD-ffsy filaments (class 2)' _pdbx_database_related.db_id EMD-27688 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8DST _pdbx_database_status.recvd_initial_deposition_date 2022-07-22 _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_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Wang, F.' 1 0000-0003-1008-663X 'Guo, J.' 2 ? 'Xu, B.' 3 ? 'Egelman, E.H.' 4 ? # _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 'Nat Nanotechnol' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1748-3395 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 18 _citation.language ? _citation.page_first 1094 _citation.page_last 1104 _citation.title 'Cell spheroid creation by transcytotic intercellular gelation.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41565-023-01401-7 _citation.pdbx_database_id_PubMed 37217766 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Guo, J.' 1 ? primary 'Wang, F.' 2 ? primary 'Huang, Y.' 3 ? primary 'He, H.' 4 ? primary 'Tan, W.' 5 ? primary 'Yi, M.' 6 ? primary 'Egelman, E.H.' 7 ? primary 'Xu, B.' 8 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'NBD-ffsy peptide' _entity.formula_weight 796.783 _entity.pdbx_number_of_molecules 6 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(D)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(UQ4)(DPN)(DPN)(DSN)(DTY)' _entity_poly.pdbx_seq_one_letter_code_can XFFSY _entity_poly.pdbx_strand_id A,B,C,D,E,F _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 UQ4 n 1 2 DPN n 1 3 DPN n 1 4 DSN n 1 5 DTY n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 5 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8DST _struct_ref.pdbx_db_accession 8DST _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 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 8DST A 1 ? 5 ? 8DST 1 ? 5 ? 1 5 2 1 8DST B 1 ? 5 ? 8DST 1 ? 5 ? 1 5 3 1 8DST C 1 ? 5 ? 8DST 1 ? 5 ? 1 5 4 1 8DST D 1 ? 5 ? 8DST 1 ? 5 ? 1 5 5 1 8DST E 1 ? 5 ? 8DST 1 ? 5 ? 1 5 6 1 8DST F 1 ? 5 ? 8DST 1 ? 5 ? 1 5 # 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 DPN 'D-peptide linking' . D-PHENYLALANINE ? 'C9 H11 N O2' 165.189 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 DTY 'D-peptide linking' . D-TYROSINE ? 'C9 H11 N O3' 181.189 UQ4 non-polymer . 'N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-beta-alanine' ? 'C9 H8 N4 O5' 252.184 # _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 8DST _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 8DST _struct.title 'Cryo-EM of NBD-ffsy filaments (class 2)' _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 8DST _struct_keywords.text 'transcytosis, hydrogel, peptides, nanofibers, spheroids, self-assembly peptide filament, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # 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 1 ? C N N 1 ? D N N 1 ? E N N 1 ? F N N 1 ? # 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 covale1 covale both ? A UQ4 1 C02 ? ? ? 1_555 A DPN 2 N ? ? A UQ4 1 A DPN 2 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale2 covale both ? A DPN 2 C ? ? ? 1_555 A DPN 3 N ? ? A DPN 2 A DPN 3 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale3 covale both ? A DPN 3 C ? ? ? 1_555 A DSN 4 N ? ? A DPN 3 A DSN 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale4 covale both ? A DSN 4 C ? ? ? 1_555 A DTY 5 N ? ? A DSN 4 A DTY 5 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale5 covale both ? B UQ4 1 C02 ? ? ? 1_555 B DPN 2 N ? ? B UQ4 1 B DPN 2 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale6 covale both ? B DPN 2 C ? ? ? 1_555 B DPN 3 N ? ? B DPN 2 B DPN 3 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? B DPN 3 C ? ? ? 1_555 B DSN 4 N ? ? B DPN 3 B DSN 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale8 covale both ? B DSN 4 C ? ? ? 1_555 B DTY 5 N ? ? B DSN 4 B DTY 5 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale9 covale both ? C UQ4 1 C02 ? ? ? 1_555 C DPN 2 N ? ? C UQ4 1 C DPN 2 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale10 covale both ? C DPN 2 C ? ? ? 1_555 C DPN 3 N ? ? C DPN 2 C DPN 3 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale11 covale both ? C DPN 3 C ? ? ? 1_555 C DSN 4 N ? ? C DPN 3 C DSN 4 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale12 covale both ? C DSN 4 C ? ? ? 1_555 C DTY 5 N ? ? C DSN 4 C DTY 5 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale13 covale both ? D UQ4 1 C02 ? ? ? 1_555 D DPN 2 N ? ? D UQ4 1 D DPN 2 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale14 covale both ? D DPN 2 C ? ? ? 1_555 D DPN 3 N ? ? D DPN 2 D DPN 3 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale15 covale both ? D DPN 3 C ? ? ? 1_555 D DSN 4 N ? ? D DPN 3 D DSN 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale16 covale both ? D DSN 4 C ? ? ? 1_555 D DTY 5 N ? ? D DSN 4 D DTY 5 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale17 covale both ? E UQ4 1 C02 ? ? ? 1_555 E DPN 2 N ? ? E UQ4 1 E DPN 2 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale18 covale both ? E DPN 2 C ? ? ? 1_555 E DPN 3 N ? ? E DPN 2 E DPN 3 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale19 covale both ? E DPN 3 C ? ? ? 1_555 E DSN 4 N ? ? E DPN 3 E DSN 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale20 covale both ? E DSN 4 C ? ? ? 1_555 E DTY 5 N ? ? E DSN 4 E DTY 5 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale21 covale both ? F UQ4 1 C02 ? ? ? 1_555 F DPN 2 N ? ? F UQ4 1 F DPN 2 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale22 covale both ? F DPN 2 C ? ? ? 1_555 F DPN 3 N ? ? F DPN 2 F DPN 3 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale23 covale both ? F DPN 3 C ? ? ? 1_555 F DSN 4 N ? ? F DPN 3 F DSN 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale24 covale both ? F DSN 4 C ? ? ? 1_555 F DTY 5 N ? ? F DSN 4 F DTY 5 1_555 ? ? ? ? ? ? ? 1.325 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8DST _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 # 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 UQ4 1 1 1 UQ4 UQ4 A . n A 1 2 DPN 2 2 2 DPN DPN A . n A 1 3 DPN 3 3 3 DPN DPN A . n A 1 4 DSN 4 4 4 DSN DSN A . n A 1 5 DTY 5 5 5 DTY DTY A . n B 1 1 UQ4 1 1 1 UQ4 UQ4 B . n B 1 2 DPN 2 2 2 DPN DPN B . n B 1 3 DPN 3 3 3 DPN DPN B . n B 1 4 DSN 4 4 4 DSN DSN B . n B 1 5 DTY 5 5 5 DTY DTY B . n C 1 1 UQ4 1 1 1 UQ4 UQ4 C . n C 1 2 DPN 2 2 2 DPN DPN C . n C 1 3 DPN 3 3 3 DPN DPN C . n C 1 4 DSN 4 4 4 DSN DSN C . n C 1 5 DTY 5 5 5 DTY DTY C . n D 1 1 UQ4 1 1 1 UQ4 UQ4 D . n D 1 2 DPN 2 2 2 DPN DPN D . n D 1 3 DPN 3 3 3 DPN DPN D . n D 1 4 DSN 4 4 4 DSN DSN D . n D 1 5 DTY 5 5 5 DTY DTY D . n E 1 1 UQ4 1 1 1 UQ4 UQ4 E . n E 1 2 DPN 2 2 2 DPN DPN E . n E 1 3 DPN 3 3 3 DPN DPN E . n E 1 4 DSN 4 4 4 DSN DSN E . n E 1 5 DTY 5 5 5 DTY DTY E . n F 1 1 UQ4 1 1 1 UQ4 UQ4 F . n F 1 2 DPN 2 2 2 DPN DPN F . n F 1 3 DPN 3 3 3 DPN DPN F . n F 1 4 DSN 4 4 4 DSN DSN F . n F 1 5 DTY 5 5 5 DTY DTY F . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email egelman@virginia.edu _pdbx_contact_author.name_first Edward _pdbx_contact_author.name_last Egelman _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4844-5212 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details 'UCSF CHIMERA 1.15_b42258.' _pdbx_struct_assembly.oligomeric_details 54-meric _pdbx_struct_assembly.oligomeric_count 54 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.000000 0.000000 0.000000 0.00000 -0.000000 1.000000 -0.000000 0.00000 -0.000000 0.000000 1.000000 0.00000 2 'helical symmetry operation' ? ? 0.999584 -0.028847 0.000000 0.00000 0.028847 0.999584 -0.000000 0.00002 -0.000000 0.000000 1.000000 -4.79999 3 'helical symmetry operation' ? ? 0.999584 0.028847 0.000000 0.00001 -0.028847 0.999584 0.000000 -0.00002 -0.000000 -0.000000 1.000000 4.80002 4 'helical symmetry operation' ? ? -0.524774 -0.851242 -0.000000 0.00000 0.851242 -0.524774 -0.000000 -0.00002 0.000000 -0.000000 1.000000 -4.79999 5 'helical symmetry operation' ? ? -0.500000 -0.866026 -0.000000 0.00001 0.866026 -0.500000 0.000000 -0.00000 -0.000000 0.000000 1.000000 -0.00001 6 'helical symmetry operation' ? ? -0.474810 -0.880088 -0.000000 0.00002 0.880088 -0.474810 -0.000001 -0.00002 0.000001 -0.000000 1.000000 4.79997 7 'helical symmetry operation' ? ? -0.474810 0.880088 -0.000001 0.00002 -0.880088 -0.474810 0.000000 -0.00002 -0.000000 0.000001 1.000000 -4.80001 8 'helical symmetry operation' ? ? -0.500000 0.866026 -0.000000 0.00001 -0.866026 -0.500000 -0.000000 -0.00000 -0.000000 -0.000000 1.000000 -0.00000 9 'helical symmetry operation' ? ? -0.524774 0.851242 0.000000 0.00000 -0.851242 -0.524774 -0.000001 0.00001 -0.000000 -0.000000 1.000000 4.79999 # 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 2023-05-31 2 'Structure model' 1 1 2023-06-07 3 'Structure model' 1 2 2023-09-27 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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' citation 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' citation 5 3 'Structure model' pdbx_struct_assembly # 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' '_citation.pdbx_database_id_PubMed' 2 2 'Structure model' '_citation.title' 3 3 'Structure model' '_citation.journal_volume' 4 3 'Structure model' '_citation.page_first' 5 3 'Structure model' '_citation.page_last' 6 3 'Structure model' '_pdbx_struct_assembly.details' # _pdbx_entry_details.entry_id 8DST _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _em_3d_fitting.entry_id 8DST _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 8DST _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 507178 _em_3d_reconstruction.resolution 3.2 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type HELICAL _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.euler_angles_details ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7.4 _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 'synthetic construct' _em_entity_assembly.source SYNTHETIC _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 8DST _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 2000 _em_imaging.nominal_defocus_min 1000 _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_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 8DST _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8DST _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method HELICAL _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 DPN N N N N 1 DPN CA C N R 2 DPN C C N N 3 DPN O O N N 4 DPN OXT O N N 5 DPN CB C N N 6 DPN CG C Y N 7 DPN CD1 C Y N 8 DPN CD2 C Y N 9 DPN CE1 C Y N 10 DPN CE2 C Y N 11 DPN CZ C Y N 12 DPN H H N N 13 DPN H2 H N N 14 DPN HA H N N 15 DPN HXT H N N 16 DPN HB2 H N N 17 DPN HB3 H N N 18 DPN HD1 H N N 19 DPN HD2 H N N 20 DPN HE1 H N N 21 DPN HE2 H N N 22 DPN HZ H N N 23 DSN N N N N 24 DSN CA C N R 25 DSN C C N N 26 DSN O O N N 27 DSN OXT O N N 28 DSN CB C N N 29 DSN OG O N N 30 DSN H H N N 31 DSN H2 H N N 32 DSN HA H N N 33 DSN HXT H N N 34 DSN HB2 H N N 35 DSN HB3 H N N 36 DSN HG H N N 37 DTY N N N N 38 DTY CA C N R 39 DTY C C N N 40 DTY O O N N 41 DTY CB C N N 42 DTY CG C Y N 43 DTY CD1 C Y N 44 DTY CD2 C Y N 45 DTY CE1 C Y N 46 DTY CE2 C Y N 47 DTY CZ C Y N 48 DTY OH O N N 49 DTY OXT O N N 50 DTY H H N N 51 DTY H2 H N N 52 DTY HA H N N 53 DTY HB2 H N N 54 DTY HB3 H N N 55 DTY HD1 H N N 56 DTY HD2 H N N 57 DTY HE1 H N N 58 DTY HE2 H N N 59 DTY HH H N N 60 DTY HXT H N N 61 UQ4 C02 C N N 62 UQ4 C50 C N N 63 UQ4 C51 C N N 64 UQ4 C53 C Y N 65 UQ4 C54 C Y N 66 UQ4 C55 C Y N 67 UQ4 C56 C Y N 68 UQ4 C60 C Y N 69 UQ4 C64 C Y N 70 UQ4 N52 N N N 71 UQ4 N57 N N N 72 UQ4 N61 N Y N 73 UQ4 N63 N Y N 74 UQ4 O01 O N N 75 UQ4 O58 O N N 76 UQ4 O59 O N N 77 UQ4 O62 O Y N 78 UQ4 H501 H N N 79 UQ4 H502 H N N 80 UQ4 H512 H N N 81 UQ4 H511 H N N 82 UQ4 H541 H N N 83 UQ4 H551 H N N 84 UQ4 H521 H N N 85 UQ4 OXT O N N 86 UQ4 HXT H N N 87 # 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 DPN N CA sing N N 1 DPN N H sing N N 2 DPN N H2 sing N N 3 DPN CA C sing N N 4 DPN CA CB sing N N 5 DPN CA HA sing N N 6 DPN C O doub N N 7 DPN C OXT sing N N 8 DPN OXT HXT sing N N 9 DPN CB CG sing N N 10 DPN CB HB2 sing N N 11 DPN CB HB3 sing N N 12 DPN CG CD1 doub Y N 13 DPN CG CD2 sing Y N 14 DPN CD1 CE1 sing Y N 15 DPN CD1 HD1 sing N N 16 DPN CD2 CE2 doub Y N 17 DPN CD2 HD2 sing N N 18 DPN CE1 CZ doub Y N 19 DPN CE1 HE1 sing N N 20 DPN CE2 CZ sing Y N 21 DPN CE2 HE2 sing N N 22 DPN CZ HZ sing N N 23 DSN N CA sing N N 24 DSN N H sing N N 25 DSN N H2 sing N N 26 DSN CA C sing N N 27 DSN CA CB sing N N 28 DSN CA HA sing N N 29 DSN C O doub N N 30 DSN C OXT sing N N 31 DSN OXT HXT sing N N 32 DSN CB OG sing N N 33 DSN CB HB2 sing N N 34 DSN CB HB3 sing N N 35 DSN OG HG sing N N 36 DTY N CA sing N N 37 DTY N H sing N N 38 DTY N H2 sing N N 39 DTY CA C sing N N 40 DTY CA CB sing N N 41 DTY CA HA sing N N 42 DTY C O doub N N 43 DTY C OXT sing N N 44 DTY CB CG sing N N 45 DTY CB HB2 sing N N 46 DTY CB HB3 sing N N 47 DTY CG CD1 doub Y N 48 DTY CG CD2 sing Y N 49 DTY CD1 CE1 sing Y N 50 DTY CD1 HD1 sing N N 51 DTY CD2 CE2 doub Y N 52 DTY CD2 HD2 sing N N 53 DTY CE1 CZ doub Y N 54 DTY CE1 HE1 sing N N 55 DTY CE2 CZ sing Y N 56 DTY CE2 HE2 sing N N 57 DTY CZ OH sing N N 58 DTY OH HH sing N N 59 DTY OXT HXT sing N N 60 UQ4 C02 O01 doub N N 61 UQ4 C02 C50 sing N N 62 UQ4 C50 C51 sing N N 63 UQ4 C51 N52 sing N N 64 UQ4 C53 C64 sing Y N 65 UQ4 C53 N52 sing N N 66 UQ4 C53 C54 doub Y N 67 UQ4 C54 C55 sing Y N 68 UQ4 C55 C56 doub Y N 69 UQ4 C56 C60 sing Y N 70 UQ4 C56 N57 sing N N 71 UQ4 C60 N61 doub Y N 72 UQ4 C60 C64 sing Y N 73 UQ4 C64 N63 doub Y N 74 UQ4 N57 O58 doub N N 75 UQ4 N57 O59 sing N N 76 UQ4 N61 O62 sing Y N 77 UQ4 N63 O62 sing Y N 78 UQ4 C50 H501 sing N N 79 UQ4 C50 H502 sing N N 80 UQ4 C51 H512 sing N N 81 UQ4 C51 H511 sing N N 82 UQ4 C54 H541 sing N N 83 UQ4 C55 H551 sing N N 84 UQ4 N52 H521 sing N N 85 UQ4 C02 OXT sing N N 86 UQ4 OXT HXT sing N N 87 # _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_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 32630 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'synthetic construct' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.angular_rotation_per_subunit -1.65 _em_helical_entity.axial_rise_per_subunit 4.80 _em_helical_entity.axial_symmetry C1 _em_helical_entity.details ? # _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 ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # 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' ? ? ? 1 ? ? 2 'IMAGE ACQUISITION' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? ? ? ? ? ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? ? ? 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_ _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' GM122510 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' K99GM138756 2 'National Institutes of Health/National Cancer Institute (NIH/NCI)' 'United States' CA142746 3 'National Science Foundation (NSF, United States)' 'United States' DMR-2011846 4 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support microscopy _pdbx_struct_assembly_auth_evidence.details ? #