data_6KJO # _entry.id 6KJO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 6KJO pdb_00006kjo 10.2210/pdb6kjo/pdb WWPDB D_1300013125 ? ? BMRB 11495 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details . _pdbx_database_related.db_id 11495 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 6KJO _pdbx_database_status.recvd_initial_deposition_date 2019-07-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nishida, N.' 1 ? 'Komori, Y.' 2 ? 'Takarada, O.' 3 ? 'Watanabe, A.' 4 ? 'Tamura, S.' 5 ? 'Kubo, S.' 6 ? 'Shimada, I.' 7 ? 'Kikkawa, M.' 8 ? # _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 Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 11 _citation.language ? _citation.page_first 1038 _citation.page_last 1038 _citation.title 'Structural basis for two-way communication between dynein and microtubules.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-020-14842-8 _citation.pdbx_database_id_PubMed 32098965 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nishida, N.' 1 0000-0001-9100-5218 primary 'Komori, Y.' 2 0000-0003-1860-864X primary 'Takarada, O.' 3 ? primary 'Watanabe, A.' 4 ? primary 'Tamura, S.' 5 ? primary 'Kubo, S.' 6 ? primary 'Shimada, I.' 7 0000-0001-9864-3407 primary 'Kikkawa, M.' 8 0000-0001-7656-8194 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Dynein heavy chain, cytoplasmic' _entity.formula_weight 16525.951 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation 'S3097C, V3222C' _entity.pdbx_fragment 'The microtubule-binding domain' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Dynein heavy chain,cytosolic,DYHC' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GSHMKCIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYD TTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKCLENVDPLRQE ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHMKCIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYD TTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKCLENVDPLRQE ; _entity_poly.pdbx_strand_id A _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 GLY n 1 2 SER n 1 3 HIS n 1 4 MET n 1 5 LYS n 1 6 CYS n 1 7 ILE n 1 8 GLN n 1 9 ASP n 1 10 ILE n 1 11 GLU n 1 12 PRO n 1 13 THR n 1 14 ILE n 1 15 LEU n 1 16 GLU n 1 17 ALA n 1 18 GLN n 1 19 ARG n 1 20 GLY n 1 21 VAL n 1 22 LYS n 1 23 ASN n 1 24 ILE n 1 25 LYS n 1 26 LYS n 1 27 GLN n 1 28 GLN n 1 29 LEU n 1 30 THR n 1 31 GLU n 1 32 ILE n 1 33 ARG n 1 34 SER n 1 35 MET n 1 36 VAL n 1 37 ASN n 1 38 PRO n 1 39 PRO n 1 40 SER n 1 41 GLY n 1 42 VAL n 1 43 LYS n 1 44 ILE n 1 45 VAL n 1 46 MET n 1 47 GLU n 1 48 ALA n 1 49 VAL n 1 50 CYS n 1 51 ALA n 1 52 ILE n 1 53 LEU n 1 54 GLY n 1 55 TYR n 1 56 GLN n 1 57 PHE n 1 58 SER n 1 59 ASN n 1 60 TRP n 1 61 ARG n 1 62 ASP n 1 63 ILE n 1 64 GLN n 1 65 GLN n 1 66 PHE n 1 67 ILE n 1 68 ARG n 1 69 LYS n 1 70 ASP n 1 71 ASP n 1 72 PHE n 1 73 ILE n 1 74 HIS n 1 75 ASN n 1 76 ILE n 1 77 VAL n 1 78 HIS n 1 79 TYR n 1 80 ASP n 1 81 THR n 1 82 THR n 1 83 LEU n 1 84 HIS n 1 85 MET n 1 86 LYS n 1 87 PRO n 1 88 GLN n 1 89 ILE n 1 90 ARG n 1 91 LYS n 1 92 TYR n 1 93 MET n 1 94 GLU n 1 95 GLU n 1 96 GLU n 1 97 PHE n 1 98 LEU n 1 99 SER n 1 100 ASP n 1 101 PRO n 1 102 ASN n 1 103 PHE n 1 104 THR n 1 105 TYR n 1 106 GLU n 1 107 THR n 1 108 ILE n 1 109 ASN n 1 110 ARG n 1 111 ALA n 1 112 SER n 1 113 LYS n 1 114 ALA n 1 115 CYS n 1 116 GLY n 1 117 PRO n 1 118 LEU n 1 119 TYR n 1 120 GLN n 1 121 TRP n 1 122 VAL n 1 123 ASN n 1 124 ALA n 1 125 GLN n 1 126 ILE n 1 127 ASN n 1 128 PHE n 1 129 SER n 1 130 LYS n 1 131 CYS n 1 132 LEU n 1 133 GLU n 1 134 ASN n 1 135 VAL n 1 136 ASP n 1 137 PRO n 1 138 LEU n 1 139 ARG n 1 140 GLN n 1 141 GLU 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 141 _entity_src_gen.gene_src_common_name ;Baker's yeast ; _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'DYN1, DHC1, YKR054C' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 204508 / S288c' _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 'Saccharomyces cerevisiae (strain ATCC 204508 / S288c)' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 559292 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET-15b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code DYHC_YEAST _struct_ref.pdbx_db_accession P36022 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKSIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYDTTL HMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKVLENVDPLRQE ; _struct_ref.pdbx_align_begin 3095 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6KJO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 141 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P36022 _struct_ref_seq.db_align_beg 3095 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 3232 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3095 _struct_ref_seq.pdbx_auth_seq_align_end 3232 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 6KJO GLY A 1 ? UNP P36022 ? ? 'expression tag' 3092 1 1 6KJO SER A 2 ? UNP P36022 ? ? 'expression tag' 3093 2 1 6KJO HIS A 3 ? UNP P36022 ? ? 'expression tag' 3094 3 1 6KJO CYS A 6 ? UNP P36022 SER 3097 'engineered mutation' 3097 4 1 6KJO CYS A 131 ? UNP P36022 VAL 3222 'engineered mutation' 3222 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-15N HSQC' 1 isotropic 2 1 1 '2D 1H-13C HSQC aliphatic' 1 isotropic 3 1 1 '2D 1H-13C HSQC aromatic' 1 isotropic 4 1 1 '3D HNCACB' 1 isotropic 5 1 1 '3D CBCA(CO)NH' 1 isotropic 6 1 1 '3D HBHA(CO)NH' 1 isotropic 7 1 2 '3D HCCH-COSY' 1 isotropic 8 1 2 '3D HCCH-TOCSY' 1 isotropic 9 1 1 '3D 1H-15N NOESY' 1 isotropic 10 1 2 '3D 1H-13C NOESY aliphatic' 1 isotropic 11 1 2 '3D 1H-13C NOESY aromatic' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 200 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1.0 mM [U-99% 13C; U-99% 15N] The microtubule-binding domain of cytoplasmic dynein, 90% H2O/10% D2O' '90% H2O/10% D2O' 13C15N_sample solution ? 2 '1.0 mM [U-99% 13C; U-99% 15N] The microtubule-binding domain of cytoplasmic dynein, 100% D2O' '100% D2O' 13C15N_sample_D2O solution ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 6KJO _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 2 # _pdbx_nmr_ensemble.entry_id 6KJO _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 6KJO _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' Sparky ? Goddard 2 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' TALOS ? 'Cornilescu, Delaglio and Bax' # _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 6KJO _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6KJO _struct.title 'The microtubule-binding domains of yeast cytoplasmic dynein in the low affinity state' _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 6KJO _struct_keywords.text 'Microtubule, Dynein, disulfide bond, low affinity, MOTOR PROTEIN' _struct_keywords.pdbx_keywords 'MOTOR PROTEIN' # _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 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 PRO A 12 ? ASN A 23 ? PRO A 3103 ASN A 3114 1 ? 12 HELX_P HELX_P2 AA2 LYS A 25 ? MET A 35 ? LYS A 3116 MET A 3126 1 ? 11 HELX_P HELX_P3 AA3 GLY A 41 ? LEU A 53 ? GLY A 3132 LEU A 3144 1 ? 13 HELX_P HELX_P4 AA4 ASN A 59 ? ARG A 68 ? ASN A 3150 ARG A 3159 1 ? 10 HELX_P HELX_P5 AA5 ILE A 73 ? HIS A 78 ? ILE A 3164 HIS A 3169 1 ? 6 HELX_P HELX_P6 AA6 GLN A 88 ? GLU A 95 ? GLN A 3179 GLU A 3186 1 ? 8 HELX_P HELX_P7 AA7 THR A 104 ? SER A 112 ? THR A 3195 SER A 3203 1 ? 9 HELX_P HELX_P8 AA8 CYS A 115 ? ASP A 136 ? CYS A 3206 ASP A 3227 1 ? 22 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id disulf1 _struct_conn.conn_type_id disulf _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 6 _struct_conn.ptnr1_label_atom_id SG _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 131 _struct_conn.ptnr2_label_atom_id SG _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 3097 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 3222 _struct_conn.ptnr2_symmetry 1_555 _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 2.022 _struct_conn.pdbx_value_order ? _struct_conn.pdbx_role ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6KJO _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 H N O S # 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 GLY 1 3092 3092 GLY GLY A . n A 1 2 SER 2 3093 3093 SER SER A . n A 1 3 HIS 3 3094 3094 HIS HIS A . n A 1 4 MET 4 3095 3095 MET MET A . n A 1 5 LYS 5 3096 3096 LYS LYS A . n A 1 6 CYS 6 3097 3097 CYS CYS A . n A 1 7 ILE 7 3098 3098 ILE ILE A . n A 1 8 GLN 8 3099 3099 GLN GLN A . n A 1 9 ASP 9 3100 3100 ASP ASP A . n A 1 10 ILE 10 3101 3101 ILE ILE A . n A 1 11 GLU 11 3102 3102 GLU GLU A . n A 1 12 PRO 12 3103 3103 PRO PRO A . n A 1 13 THR 13 3104 3104 THR THR A . n A 1 14 ILE 14 3105 3105 ILE ILE A . n A 1 15 LEU 15 3106 3106 LEU LEU A . n A 1 16 GLU 16 3107 3107 GLU GLU A . n A 1 17 ALA 17 3108 3108 ALA ALA A . n A 1 18 GLN 18 3109 3109 GLN GLN A . n A 1 19 ARG 19 3110 3110 ARG ARG A . n A 1 20 GLY 20 3111 3111 GLY GLY A . n A 1 21 VAL 21 3112 3112 VAL VAL A . n A 1 22 LYS 22 3113 3113 LYS LYS A . n A 1 23 ASN 23 3114 3114 ASN ASN A . n A 1 24 ILE 24 3115 3115 ILE ILE A . n A 1 25 LYS 25 3116 3116 LYS LYS A . n A 1 26 LYS 26 3117 3117 LYS LYS A . n A 1 27 GLN 27 3118 3118 GLN GLN A . n A 1 28 GLN 28 3119 3119 GLN GLN A . n A 1 29 LEU 29 3120 3120 LEU LEU A . n A 1 30 THR 30 3121 3121 THR THR A . n A 1 31 GLU 31 3122 3122 GLU GLU A . n A 1 32 ILE 32 3123 3123 ILE ILE A . n A 1 33 ARG 33 3124 3124 ARG ARG A . n A 1 34 SER 34 3125 3125 SER SER A . n A 1 35 MET 35 3126 3126 MET MET A . n A 1 36 VAL 36 3127 3127 VAL VAL A . n A 1 37 ASN 37 3128 3128 ASN ASN A . n A 1 38 PRO 38 3129 3129 PRO PRO A . n A 1 39 PRO 39 3130 3130 PRO PRO A . n A 1 40 SER 40 3131 3131 SER SER A . n A 1 41 GLY 41 3132 3132 GLY GLY A . n A 1 42 VAL 42 3133 3133 VAL VAL A . n A 1 43 LYS 43 3134 3134 LYS LYS A . n A 1 44 ILE 44 3135 3135 ILE ILE A . n A 1 45 VAL 45 3136 3136 VAL VAL A . n A 1 46 MET 46 3137 3137 MET MET A . n A 1 47 GLU 47 3138 3138 GLU GLU A . n A 1 48 ALA 48 3139 3139 ALA ALA A . n A 1 49 VAL 49 3140 3140 VAL VAL A . n A 1 50 CYS 50 3141 3141 CYS CYS A . n A 1 51 ALA 51 3142 3142 ALA ALA A . n A 1 52 ILE 52 3143 3143 ILE ILE A . n A 1 53 LEU 53 3144 3144 LEU LEU A . n A 1 54 GLY 54 3145 3145 GLY GLY A . n A 1 55 TYR 55 3146 3146 TYR TYR A . n A 1 56 GLN 56 3147 3147 GLN GLN A . n A 1 57 PHE 57 3148 3148 PHE PHE A . n A 1 58 SER 58 3149 3149 SER SER A . n A 1 59 ASN 59 3150 3150 ASN ASN A . n A 1 60 TRP 60 3151 3151 TRP TRP A . n A 1 61 ARG 61 3152 3152 ARG ARG A . n A 1 62 ASP 62 3153 3153 ASP ASP A . n A 1 63 ILE 63 3154 3154 ILE ILE A . n A 1 64 GLN 64 3155 3155 GLN GLN A . n A 1 65 GLN 65 3156 3156 GLN GLN A . n A 1 66 PHE 66 3157 3157 PHE PHE A . n A 1 67 ILE 67 3158 3158 ILE ILE A . n A 1 68 ARG 68 3159 3159 ARG ARG A . n A 1 69 LYS 69 3160 3160 LYS LYS A . n A 1 70 ASP 70 3161 3161 ASP ASP A . n A 1 71 ASP 71 3162 3162 ASP ASP A . n A 1 72 PHE 72 3163 3163 PHE PHE A . n A 1 73 ILE 73 3164 3164 ILE ILE A . n A 1 74 HIS 74 3165 3165 HIS HIS A . n A 1 75 ASN 75 3166 3166 ASN ASN A . n A 1 76 ILE 76 3167 3167 ILE ILE A . n A 1 77 VAL 77 3168 3168 VAL VAL A . n A 1 78 HIS 78 3169 3169 HIS HIS A . n A 1 79 TYR 79 3170 3170 TYR TYR A . n A 1 80 ASP 80 3171 3171 ASP ASP A . n A 1 81 THR 81 3172 3172 THR THR A . n A 1 82 THR 82 3173 3173 THR THR A . n A 1 83 LEU 83 3174 3174 LEU LEU A . n A 1 84 HIS 84 3175 3175 HIS HIS A . n A 1 85 MET 85 3176 3176 MET MET A . n A 1 86 LYS 86 3177 3177 LYS LYS A . n A 1 87 PRO 87 3178 3178 PRO PRO A . n A 1 88 GLN 88 3179 3179 GLN GLN A . n A 1 89 ILE 89 3180 3180 ILE ILE A . n A 1 90 ARG 90 3181 3181 ARG ARG A . n A 1 91 LYS 91 3182 3182 LYS LYS A . n A 1 92 TYR 92 3183 3183 TYR TYR A . n A 1 93 MET 93 3184 3184 MET MET A . n A 1 94 GLU 94 3185 3185 GLU GLU A . n A 1 95 GLU 95 3186 3186 GLU GLU A . n A 1 96 GLU 96 3187 3187 GLU GLU A . n A 1 97 PHE 97 3188 3188 PHE PHE A . n A 1 98 LEU 98 3189 3189 LEU LEU A . n A 1 99 SER 99 3190 3190 SER SER A . n A 1 100 ASP 100 3191 3191 ASP ASP A . n A 1 101 PRO 101 3192 3192 PRO PRO A . n A 1 102 ASN 102 3193 3193 ASN ASN A . n A 1 103 PHE 103 3194 3194 PHE PHE A . n A 1 104 THR 104 3195 3195 THR THR A . n A 1 105 TYR 105 3196 3196 TYR TYR A . n A 1 106 GLU 106 3197 3197 GLU GLU A . n A 1 107 THR 107 3198 3198 THR THR A . n A 1 108 ILE 108 3199 3199 ILE ILE A . n A 1 109 ASN 109 3200 3200 ASN ASN A . n A 1 110 ARG 110 3201 3201 ARG ARG A . n A 1 111 ALA 111 3202 3202 ALA ALA A . n A 1 112 SER 112 3203 3203 SER SER A . n A 1 113 LYS 113 3204 3204 LYS LYS A . n A 1 114 ALA 114 3205 3205 ALA ALA A . n A 1 115 CYS 115 3206 3206 CYS CYS A . n A 1 116 GLY 116 3207 3207 GLY GLY A . n A 1 117 PRO 117 3208 3208 PRO PRO A . n A 1 118 LEU 118 3209 3209 LEU LEU A . n A 1 119 TYR 119 3210 3210 TYR TYR A . n A 1 120 GLN 120 3211 3211 GLN GLN A . n A 1 121 TRP 121 3212 3212 TRP TRP A . n A 1 122 VAL 122 3213 3213 VAL VAL A . n A 1 123 ASN 123 3214 3214 ASN ASN A . n A 1 124 ALA 124 3215 3215 ALA ALA A . n A 1 125 GLN 125 3216 3216 GLN GLN A . n A 1 126 ILE 126 3217 3217 ILE ILE A . n A 1 127 ASN 127 3218 3218 ASN ASN A . n A 1 128 PHE 128 3219 3219 PHE PHE A . n A 1 129 SER 129 3220 3220 SER SER A . n A 1 130 LYS 130 3221 3221 LYS LYS A . n A 1 131 CYS 131 3222 3222 CYS CYS A . n A 1 132 LEU 132 3223 3223 LEU LEU A . n A 1 133 GLU 133 3224 3224 GLU GLU A . n A 1 134 ASN 134 3225 3225 ASN ASN A . n A 1 135 VAL 135 3226 3226 VAL VAL A . n A 1 136 ASP 136 3227 3227 ASP ASP A . n A 1 137 PRO 137 3228 3228 PRO PRO A . n A 1 138 LEU 138 3229 3229 LEU LEU A . n A 1 139 ARG 139 3230 3230 ARG ARG A . n A 1 140 GLN 140 3231 3231 GLN GLN A . n A 1 141 GLU 141 3232 3232 GLU GLU A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # 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)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 9580 ? # _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_ _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 2020-03-18 2 'Structure model' 1 1 2023-06-14 # _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 2 'Structure model' Other # 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' database_2 2 2 'Structure model' pdbx_database_status # 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' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 'The microtubule-binding domain of cytoplasmic dynein' 1.0 ? mM '[U-99% 13C; U-99% 15N]' 2 'The microtubule-binding domain of cytoplasmic dynein' 1.0 ? mM '[U-99% 13C; U-99% 15N]' # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 3102 ? ? -24.60 127.67 2 1 MET A 3126 ? ? -59.01 108.87 3 1 SER A 3131 ? ? -49.53 97.98 4 1 SER A 3149 ? ? -146.12 29.95 5 1 MET A 3176 ? ? -56.30 -171.16 6 1 GLU A 3186 ? ? -5.71 -89.22 7 1 SER A 3203 ? ? -171.42 134.35 8 1 LEU A 3229 ? ? 69.57 136.23 9 2 GLU A 3102 ? ? -26.57 130.73 10 2 LYS A 3116 ? ? -68.96 -169.58 11 2 SER A 3131 ? ? -58.75 94.18 12 2 GLN A 3147 ? ? -70.19 -165.79 13 2 LYS A 3177 ? ? 175.21 -52.43 14 2 GLU A 3186 ? ? -66.73 -72.09 15 2 ASP A 3191 ? ? -37.88 116.62 16 2 ASN A 3225 ? ? -149.04 51.38 17 2 ASP A 3227 ? ? -47.56 106.09 18 2 ARG A 3230 ? ? 51.87 79.11 19 3 HIS A 3094 ? ? 47.38 74.25 20 3 GLU A 3102 ? ? -24.30 129.23 21 3 SER A 3131 ? ? -57.75 93.42 22 3 GLN A 3147 ? ? -177.29 109.28 23 3 THR A 3173 ? ? -37.84 -38.57 24 3 MET A 3176 ? ? 77.18 -44.61 25 3 LYS A 3177 ? ? 60.48 103.74 26 3 GLU A 3187 ? ? -164.82 -18.70 27 3 ASP A 3191 ? ? -40.31 107.83 28 4 HIS A 3094 ? ? 58.36 -150.30 29 4 GLU A 3102 ? ? -23.52 131.28 30 4 PRO A 3103 ? ? -59.13 -7.24 31 4 SER A 3131 ? ? -53.77 96.10 32 4 SER A 3149 ? ? -161.70 40.17 33 4 THR A 3173 ? ? -29.79 -46.08 34 4 LEU A 3174 ? ? -44.06 155.19 35 4 MET A 3176 ? ? 69.65 148.73 36 4 LYS A 3177 ? ? -163.32 79.40 37 4 PRO A 3178 ? ? -75.84 40.46 38 4 GLU A 3187 ? ? -168.91 -9.31 39 4 SER A 3203 ? ? -170.25 133.50 40 5 ILE A 3098 ? ? -39.65 -34.06 41 5 GLU A 3102 ? ? -27.04 129.19 42 5 LYS A 3116 ? ? 175.01 -178.82 43 5 LYS A 3117 ? ? 69.28 -128.14 44 5 ASN A 3128 ? ? -119.55 77.84 45 5 SER A 3131 ? ? -58.75 97.13 46 5 SER A 3149 ? ? -164.40 34.41 47 5 LEU A 3174 ? ? 96.63 86.16 48 5 GLN A 3179 ? ? -69.79 1.31 49 5 GLU A 3187 ? ? -171.80 -4.38 50 5 ASP A 3191 ? ? -35.09 121.70 51 5 VAL A 3226 ? ? -42.97 151.70 52 5 LEU A 3229 ? ? -140.11 16.07 53 5 ARG A 3230 ? ? -124.79 -64.42 54 6 MET A 3095 ? ? -104.82 -65.01 55 6 CYS A 3097 ? ? -173.19 -171.77 56 6 GLN A 3099 ? ? -58.17 -70.52 57 6 GLU A 3102 ? ? -23.46 123.99 58 6 SER A 3131 ? ? -56.85 97.29 59 6 SER A 3149 ? ? -178.44 42.35 60 6 MET A 3176 ? ? 71.20 81.73 61 6 GLU A 3187 ? ? -158.70 -3.02 62 6 PHE A 3194 ? ? -104.01 64.12 63 6 ASN A 3225 ? ? -143.10 34.31 64 7 GLU A 3102 ? ? -30.73 128.26 65 7 SER A 3131 ? ? -55.71 95.50 66 7 GLN A 3147 ? ? -73.75 -156.66 67 7 THR A 3173 ? ? -35.95 -39.40 68 7 LEU A 3174 ? ? -40.91 157.17 69 7 MET A 3176 ? ? -35.50 113.87 70 7 GLU A 3186 ? ? -5.97 -80.37 71 8 SER A 3093 ? ? -140.22 -63.70 72 8 GLU A 3102 ? ? -30.89 130.05 73 8 SER A 3131 ? ? -58.68 94.08 74 8 GLN A 3147 ? ? -111.21 72.53 75 8 SER A 3149 ? ? -142.81 28.55 76 8 LEU A 3174 ? ? -107.08 63.22 77 8 MET A 3176 ? ? 105.30 36.33 78 8 LYS A 3177 ? ? 61.54 146.12 79 8 GLU A 3187 ? ? -168.63 -9.12 80 8 ASP A 3191 ? ? -39.48 112.47 81 8 LEU A 3229 ? ? -156.59 64.15 82 9 SER A 3093 ? ? -153.35 75.22 83 9 LYS A 3096 ? ? -173.09 114.84 84 9 GLU A 3102 ? ? -25.30 128.99 85 9 MET A 3126 ? ? -57.42 98.06 86 9 SER A 3131 ? ? 163.50 -46.61 87 9 GLN A 3147 ? ? -72.43 -159.13 88 9 TYR A 3170 ? ? -48.63 108.73 89 9 MET A 3176 ? ? 66.71 97.75 90 9 LYS A 3177 ? ? 60.45 63.96 91 9 GLU A 3187 ? ? -164.54 -17.48 92 9 PHE A 3194 ? ? -96.46 58.37 93 10 GLU A 3102 ? ? -27.75 129.08 94 10 SER A 3131 ? ? -59.70 91.45 95 10 GLN A 3147 ? ? -119.68 74.46 96 10 THR A 3173 ? ? -6.60 -79.85 97 10 MET A 3176 ? ? 130.37 152.68 98 10 GLU A 3187 ? ? -170.84 -12.29 99 10 VAL A 3226 ? ? -141.26 -46.50 100 10 ARG A 3230 ? ? -98.42 51.31 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science' Japan 26119005 1 'Japan Society for the Promotion of Science' Japan 21121002 2 'Japan Science and Technology' Japan JPMJCR14M1 3 'Japan Agency for Medical Research and Development (AMED)' Japan JP19am01011115 4 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #