data_6NHY # _entry.id 6NHY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 6NHY pdb_00006nhy 10.2210/pdb6nhy/pdb WWPDB D_1000238767 ? ? BMRB 30554 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only' _pdbx_database_related.db_id 30554 _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 6NHY _pdbx_database_status.recvd_initial_deposition_date 2018-12-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Chou, J.J.' 1 ? 'Pan, L.' 2 ? 'Zhao, L.' 3 ? 'Chen, W.' 4 ? 'Piai, A.' 5 ? 'Fu, T.' 6 ? 'Wu, H.' 7 ? 'Liu, Z.' 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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Cell _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1097-4172 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 176 _citation.language ? _citation.page_first 1477 _citation.page_last 1489.e14 _citation.title 'Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling.' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.cell.2019.02.001 _citation.pdbx_database_id_PubMed 30827683 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pan, L.' 1 ? primary 'Fu, T.M.' 2 ? primary 'Zhao, W.' 3 ? primary 'Zhao, L.' 4 ? primary 'Chen, W.' 5 ? primary 'Qiu, C.' 6 ? primary 'Liu, W.' 7 ? primary 'Liu, Z.' 8 ? primary 'Piai, A.' 9 ? primary 'Fu, Q.' 10 ? primary 'Chen, S.' 11 ? primary 'Wu, H.' 12 ? primary 'Chou, J.J.' 13 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Tumor necrosis factor receptor superfamily member 10B' _entity.formula_weight 3831.821 _entity.pdbx_number_of_molecules 3 _entity.pdbx_ec ? _entity.pdbx_mutation G217Y _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Death receptor 5,TNF-related apoptosis-inducing ligand receptor 2,TRAIL-R2' # _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 MPGSLSGIIIYVTVAAVVLIVAVFVCKSLLWKKVLP _entity_poly.pdbx_seq_one_letter_code_can MPGSLSGIIIYVTVAAVVLIVAVFVCKSLLWKKVLP _entity_poly.pdbx_strand_id A,B,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 MET n 1 2 PRO n 1 3 GLY n 1 4 SER n 1 5 LEU n 1 6 SER n 1 7 GLY n 1 8 ILE n 1 9 ILE n 1 10 ILE n 1 11 TYR n 1 12 VAL n 1 13 THR n 1 14 VAL n 1 15 ALA n 1 16 ALA n 1 17 VAL n 1 18 VAL n 1 19 LEU n 1 20 ILE n 1 21 VAL n 1 22 ALA n 1 23 VAL n 1 24 PHE n 1 25 VAL n 1 26 CYS n 1 27 LYS n 1 28 SER n 1 29 LEU n 1 30 LEU n 1 31 TRP n 1 32 LYS n 1 33 LYS n 1 34 VAL n 1 35 LEU n 1 36 PRO 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 36 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21 (DE3)' _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 pMM-LR6 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TR10B_HUMAN _struct_ref.pdbx_db_accession O14763 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code PCSLSGIIIGVTVAAVVLIVAVFVCKSLLWKKVLP _struct_ref.pdbx_align_begin 208 # 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 6NHY A 2 ? 36 ? O14763 208 ? 242 ? 208 242 2 1 6NHY B 2 ? 36 ? O14763 208 ? 242 ? 208 242 3 1 6NHY C 2 ? 36 ? O14763 208 ? 242 ? 208 242 # 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 6NHY MET A 1 ? UNP O14763 ? ? 'initiating methionine' 207 1 1 6NHY GLY A 3 ? UNP O14763 CYS 209 conflict 209 2 1 6NHY TYR A 11 ? UNP O14763 GLY 217 'engineered mutation' 217 3 2 6NHY MET B 1 ? UNP O14763 ? ? 'initiating methionine' 207 4 2 6NHY GLY B 3 ? UNP O14763 CYS 209 conflict 209 5 2 6NHY TYR B 11 ? UNP O14763 GLY 217 'engineered mutation' 217 6 3 6NHY MET C 1 ? UNP O14763 ? ? 'initiating methionine' 207 7 3 6NHY GLY C 3 ? UNP O14763 CYS 209 conflict 209 8 3 6NHY TYR C 11 ? UNP O14763 GLY 217 'engineered mutation' 217 9 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 'TROSY HSQC' 1 isotropic 2 1 1 'TROSY HNCA' 1 isotropic 3 1 1 'TROSY HNCOCA' 1 isotropic 4 1 1 'TROSY HNCACO' 1 isotropic 5 1 1 'TROSY HNCO' 1 isotropic 6 1 1 '3D 15N NOE-TROSY-HSQC' 2 isotropic 7 1 2 '3D 15N NOE-TROSY-HSQC' 3 isotropic 8 1 2 '2D 1H-13C HSQC' 3 isotropic 9 1 2 '3D 13C NOE-HSQC' 3 isotropic 10 1 3 '2D 1H-13C HSQC' 3 isotropic 11 1 3 '3D 15N NOE-TROSY-HSQC' 3 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _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 ;0.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O ; '95% H2O/5% D2O' NCD_sample bicelle '(15N, 13C, 85% 2H) labeled sample for backbone resonance assignment' 2 ;0.8 mM [U-13C; U-15N] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O ; '95% H2O/5% D2O' NC_sample bicelle '(15N, 13C) labeled sample for NOE assignments' 3 ;0.4 mM [15%-13C; U-15N; H-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O ; '95% H2O/5% D2O' mixed_sample bicelle 'Isotope mixed sample for detecting inter-chain NOEs' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 AVANCE ? Bruker 600 'cryogenic probe' 2 AVANCE ? Bruker 750 'cryogenic probe' 3 AVANCE ? Bruker 900 'cryogenic probe' # _pdbx_nmr_refine.entry_id 6NHY _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 6NHY _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _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 6NHY _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 2 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' XEASY ? 'Bartels et al.' 4 processing NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 5 'data analysis' 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 6NHY _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6NHY _struct.title 'Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only' _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 6NHY _struct_keywords.text 'transmembrane helix trimer, IMMUNE SYSTEM' _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' # 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 ? # 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 SER A 4 ? TRP A 31 ? SER A 210 TRP A 237 1 ? 28 HELX_P HELX_P2 AA2 LEU B 5 ? TRP B 31 ? LEU B 211 TRP B 237 1 ? 27 HELX_P HELX_P3 AA3 SER C 4 ? LYS C 32 ? SER C 210 LYS C 238 1 ? 29 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 6NHY _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 # 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 MET 1 207 207 MET MET A . n A 1 2 PRO 2 208 208 PRO PRO A . n A 1 3 GLY 3 209 209 GLY GLY A . n A 1 4 SER 4 210 210 SER SER A . n A 1 5 LEU 5 211 211 LEU LEU A . n A 1 6 SER 6 212 212 SER SER A . n A 1 7 GLY 7 213 213 GLY GLY A . n A 1 8 ILE 8 214 214 ILE ILE A . n A 1 9 ILE 9 215 215 ILE ILE A . n A 1 10 ILE 10 216 216 ILE ILE A . n A 1 11 TYR 11 217 217 TYR TYR A . n A 1 12 VAL 12 218 218 VAL VAL A . n A 1 13 THR 13 219 219 THR THR A . n A 1 14 VAL 14 220 220 VAL VAL A . n A 1 15 ALA 15 221 221 ALA ALA A . n A 1 16 ALA 16 222 222 ALA ALA A . n A 1 17 VAL 17 223 223 VAL VAL A . n A 1 18 VAL 18 224 224 VAL VAL A . n A 1 19 LEU 19 225 225 LEU LEU A . n A 1 20 ILE 20 226 226 ILE ILE A . n A 1 21 VAL 21 227 227 VAL VAL A . n A 1 22 ALA 22 228 228 ALA ALA A . n A 1 23 VAL 23 229 229 VAL VAL A . n A 1 24 PHE 24 230 230 PHE PHE A . n A 1 25 VAL 25 231 231 VAL VAL A . n A 1 26 CYS 26 232 232 CYS CYS A . n A 1 27 LYS 27 233 233 LYS LYS A . n A 1 28 SER 28 234 234 SER SER A . n A 1 29 LEU 29 235 235 LEU LEU A . n A 1 30 LEU 30 236 236 LEU LEU A . n A 1 31 TRP 31 237 237 TRP TRP A . n A 1 32 LYS 32 238 238 LYS LYS A . n A 1 33 LYS 33 239 239 LYS LYS A . n A 1 34 VAL 34 240 240 VAL VAL A . n A 1 35 LEU 35 241 241 LEU LEU A . n A 1 36 PRO 36 242 242 PRO PRO A . n B 1 1 MET 1 207 207 MET MET B . n B 1 2 PRO 2 208 208 PRO PRO B . n B 1 3 GLY 3 209 209 GLY GLY B . n B 1 4 SER 4 210 210 SER SER B . n B 1 5 LEU 5 211 211 LEU LEU B . n B 1 6 SER 6 212 212 SER SER B . n B 1 7 GLY 7 213 213 GLY GLY B . n B 1 8 ILE 8 214 214 ILE ILE B . n B 1 9 ILE 9 215 215 ILE ILE B . n B 1 10 ILE 10 216 216 ILE ILE B . n B 1 11 TYR 11 217 217 TYR TYR B . n B 1 12 VAL 12 218 218 VAL VAL B . n B 1 13 THR 13 219 219 THR THR B . n B 1 14 VAL 14 220 220 VAL VAL B . n B 1 15 ALA 15 221 221 ALA ALA B . n B 1 16 ALA 16 222 222 ALA ALA B . n B 1 17 VAL 17 223 223 VAL VAL B . n B 1 18 VAL 18 224 224 VAL VAL B . n B 1 19 LEU 19 225 225 LEU LEU B . n B 1 20 ILE 20 226 226 ILE ILE B . n B 1 21 VAL 21 227 227 VAL VAL B . n B 1 22 ALA 22 228 228 ALA ALA B . n B 1 23 VAL 23 229 229 VAL VAL B . n B 1 24 PHE 24 230 230 PHE PHE B . n B 1 25 VAL 25 231 231 VAL VAL B . n B 1 26 CYS 26 232 232 CYS CYS B . n B 1 27 LYS 27 233 233 LYS LYS B . n B 1 28 SER 28 234 234 SER SER B . n B 1 29 LEU 29 235 235 LEU LEU B . n B 1 30 LEU 30 236 236 LEU LEU B . n B 1 31 TRP 31 237 237 TRP TRP B . n B 1 32 LYS 32 238 238 LYS LYS B . n B 1 33 LYS 33 239 239 LYS LYS B . n B 1 34 VAL 34 240 240 VAL VAL B . n B 1 35 LEU 35 241 241 LEU LEU B . n B 1 36 PRO 36 242 242 PRO PRO B . n C 1 1 MET 1 207 207 MET MET C . n C 1 2 PRO 2 208 208 PRO PRO C . n C 1 3 GLY 3 209 209 GLY GLY C . n C 1 4 SER 4 210 210 SER SER C . n C 1 5 LEU 5 211 211 LEU LEU C . n C 1 6 SER 6 212 212 SER SER C . n C 1 7 GLY 7 213 213 GLY GLY C . n C 1 8 ILE 8 214 214 ILE ILE C . n C 1 9 ILE 9 215 215 ILE ILE C . n C 1 10 ILE 10 216 216 ILE ILE C . n C 1 11 TYR 11 217 217 TYR TYR C . n C 1 12 VAL 12 218 218 VAL VAL C . n C 1 13 THR 13 219 219 THR THR C . n C 1 14 VAL 14 220 220 VAL VAL C . n C 1 15 ALA 15 221 221 ALA ALA C . n C 1 16 ALA 16 222 222 ALA ALA C . n C 1 17 VAL 17 223 223 VAL VAL C . n C 1 18 VAL 18 224 224 VAL VAL C . n C 1 19 LEU 19 225 225 LEU LEU C . n C 1 20 ILE 20 226 226 ILE ILE C . n C 1 21 VAL 21 227 227 VAL VAL C . n C 1 22 ALA 22 228 228 ALA ALA C . n C 1 23 VAL 23 229 229 VAL VAL C . n C 1 24 PHE 24 230 230 PHE PHE C . n C 1 25 VAL 25 231 231 VAL VAL C . n C 1 26 CYS 26 232 232 CYS CYS C . n C 1 27 LYS 27 233 233 LYS LYS C . n C 1 28 SER 28 234 234 SER SER C . n C 1 29 LEU 29 235 235 LEU LEU C . n C 1 30 LEU 30 236 236 LEU LEU C . n C 1 31 TRP 31 237 237 TRP TRP C . n C 1 32 LYS 32 238 238 LYS LYS C . n C 1 33 LYS 33 239 239 LYS LYS C . n C 1 34 VAL 34 240 240 VAL VAL C . n C 1 35 LEU 35 241 241 LEU LEU C . n C 1 36 PRO 36 242 242 PRO PRO C . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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)' 1380 ? 1 MORE -21 ? 1 'SSA (A^2)' 10660 ? # _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 2019-02-27 2 'Structure model' 1 1 2019-03-20 3 'Structure model' 1 2 2020-01-01 4 'Structure model' 1 3 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Author supporting evidence' 4 3 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 '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' citation 2 2 'Structure model' citation_author 3 3 'Structure model' pdbx_audit_support 4 3 'Structure model' pdbx_nmr_spectrometer 5 4 'Structure model' database_2 6 4 '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' '_citation.journal_abbrev' 2 2 'Structure model' '_citation.journal_id_CSD' 3 2 'Structure model' '_citation.journal_id_ISSN' 4 2 'Structure model' '_citation.journal_volume' 5 2 'Structure model' '_citation.page_first' 6 2 'Structure model' '_citation.page_last' 7 2 'Structure model' '_citation.pdbx_database_id_DOI' 8 2 'Structure model' '_citation.pdbx_database_id_PubMed' 9 2 'Structure model' '_citation.title' 10 2 'Structure model' '_citation.year' 11 2 'Structure model' '_citation_author.name' 12 3 'Structure model' '_pdbx_audit_support.funding_organization' 13 3 'Structure model' '_pdbx_nmr_spectrometer.model' 14 4 'Structure model' '_database_2.pdbx_DOI' 15 4 'Structure model' '_database_2.pdbx_database_accession' 16 4 '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 'Transmembrane Domain of DR5 Mutant G217Y' 0.8 ? mM '[U-13C; U-15N; 85%-2H]' 1 DMPC 50 ? mM 'natural abundance' 1 DHPC 100 ? mM 'natural abundance' 1 'sodium phosphate' 20 ? mM 'natural abundance' 2 'Transmembrane Domain of DR5 Mutant G217Y' 0.8 ? mM '[U-13C; U-15N]' 2 DMPC 50 ? mM '[acyl chain U-2H]' 2 DHPC 100 ? mM '[acyl chain U-2H]' 2 'sodium phosphate' 20 ? mM 'natural abundance' 3 'Transmembrane Domain of DR5 Mutant G217Y' 0.4 ? mM '[15%-13C; U-15N; H-2H]' 3 DMPC 50 ? mM '[acyl chain U-2H]' 3 DHPC 100 ? mM '[acyl chain U-2H]' 3 'sodium phosphate' 20 ? mM 'natural abundance' # 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 SER A 210 ? ? -166.46 35.63 2 1 LYS A 239 ? ? -53.17 -9.54 3 1 PRO B 208 ? ? -59.74 -76.95 4 1 SER B 210 ? ? -158.90 21.03 5 1 PRO C 208 ? ? -76.31 42.03 6 1 SER C 210 ? ? -167.77 71.14 7 2 PRO A 208 ? ? -72.96 -167.55 8 2 LEU A 211 ? ? -159.98 -37.71 9 2 LYS A 239 ? ? 74.19 -18.12 10 2 SER B 210 ? ? 61.62 149.23 11 2 LEU B 211 ? ? -170.55 30.23 12 2 LYS B 239 ? ? -146.02 -52.30 13 2 SER C 210 ? ? -166.76 45.10 14 2 LYS C 239 ? ? -158.37 -67.99 15 3 PRO A 208 ? ? -72.59 -166.17 16 3 SER A 210 ? ? -56.62 89.75 17 3 LYS A 239 ? ? -167.12 -34.64 18 3 LEU C 211 ? ? -166.48 -45.58 19 3 LYS C 238 ? ? -132.36 -53.66 20 3 LYS C 239 ? ? 65.21 -19.86 21 4 SER A 210 ? ? -167.93 80.31 22 4 LEU A 211 ? ? -161.63 -0.83 23 4 SER B 210 ? ? -163.56 37.63 24 4 LEU B 211 ? ? 54.70 9.07 25 5 SER A 210 ? ? -169.56 58.51 26 5 LEU A 211 ? ? -145.51 -9.91 27 5 SER B 210 ? ? 59.06 121.99 28 5 LEU B 211 ? ? -165.39 -49.13 29 5 LYS B 239 ? ? 72.33 -7.87 30 5 SER C 210 ? ? 56.92 174.18 31 5 LEU C 211 ? ? 76.23 -33.56 32 5 LYS C 239 ? ? 82.44 9.77 33 6 LEU A 211 ? ? 65.31 -0.37 34 6 SER B 210 ? ? -166.73 76.75 35 6 LYS C 238 ? ? 33.70 36.58 36 6 LYS C 239 ? ? 70.52 -7.37 37 7 SER A 210 ? ? 58.19 167.12 38 7 LYS A 239 ? ? 71.72 -8.68 39 7 LEU B 211 ? ? 82.70 -36.98 40 8 LEU A 211 ? ? -163.08 -48.31 41 8 LEU B 211 ? ? -152.27 23.74 42 8 LYS B 238 ? ? -136.74 -56.90 43 8 LYS B 239 ? ? 71.25 -2.74 44 8 LEU C 211 ? ? -170.37 46.48 45 9 LEU A 211 ? ? 56.94 9.14 46 9 LYS A 239 ? ? 92.07 -17.70 47 9 SER B 210 ? ? -67.28 72.32 48 9 LEU B 211 ? ? -162.60 -51.31 49 9 LEU C 211 ? ? -165.12 -51.27 50 9 LYS C 238 ? ? -139.93 -62.77 51 9 LYS C 239 ? ? 70.77 -26.37 52 10 SER A 210 ? ? -167.63 44.43 53 10 LYS A 239 ? ? 73.09 -3.95 54 10 SER B 210 ? ? -169.10 56.41 55 10 LYS B 238 ? ? -143.07 31.51 56 10 LYS B 239 ? ? -162.21 -60.94 57 10 PRO C 208 ? ? -89.07 47.38 58 11 LYS A 239 ? ? 64.97 -24.10 59 11 LYS B 239 ? ? 178.01 -34.44 60 12 SER A 210 ? ? 60.21 156.87 61 12 LEU A 211 ? ? -165.47 -53.57 62 12 LEU B 211 ? ? -167.37 21.60 63 12 SER C 210 ? ? 58.38 159.54 64 13 SER A 210 ? ? 56.45 77.67 65 13 LEU A 211 ? ? -161.30 21.32 66 13 LYS B 238 ? ? 55.09 13.22 67 13 SER C 210 ? ? 57.28 176.89 68 13 LEU C 211 ? ? 69.92 -32.30 69 14 LEU A 211 ? ? 66.60 -9.81 70 14 PRO B 208 ? ? -51.39 175.12 71 14 LEU B 211 ? ? -165.63 -48.20 72 14 LYS B 239 ? ? 82.87 48.65 73 14 SER C 210 ? ? 56.57 100.47 74 14 LEU C 211 ? ? -148.62 -5.43 75 15 LYS A 239 ? ? -160.28 -22.75 76 15 LYS B 239 ? ? -165.79 -11.58 77 15 PRO C 208 ? ? -51.06 104.08 78 15 SER C 210 ? ? 55.56 -177.62 79 15 LEU C 211 ? ? 66.85 -1.22 80 15 LYS C 238 ? ? 95.19 59.55 # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM116898 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'assay for oligomerization' _pdbx_struct_assembly_auth_evidence.details ;OG-label method (Chen et al: The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure, 26(4):627-634 (2018).) ; #