data_30554 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only ; _BMRB_accession_number 30554 _BMRB_flat_file_name bmr30554.str _Entry_type original _Submission_date 2018-12-24 _Accession_date 2018-12-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chou J. J. . 2 Pan L. . . 3 Zhao L. . . 4 Chen W. . . 5 Piai A. . . 6 Fu T. . . 7 Wu H. . . 8 Liu Z. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 33 "13C chemical shifts" 67 "15N chemical shifts" 33 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-08 update BMRB 'update entry citation' 2019-02-22 original author 'original release' stop_ _Original_release_date 2019-02-15 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30827683 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pan Liqiang . . 2 Fu Tian-Min M. . 3 Zhao Wenbin . . 4 Zhao Linlin . . 5 Chen Wen . . 6 Qiu Chixiao . . 7 Liu Wenhui . . 8 Liu Zhijun . . 9 Piai Alessandro . . 10 Fu Qingshan . . 11 Chen Shuqing . . 12 Wu Hao . . 13 Chou James J. . stop_ _Journal_abbreviation Cell _Journal_name_full Cell _Journal_volume 176 _Journal_issue 6 _Journal_ISSN 1097-4172 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1477 _Page_last 1489.e14 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Tumor necrosis factor receptor superfamily member 10B' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_1, 3' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 3831.821 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; MPGSLSGIIIYVTVAAVVLI VAVFVCKSLLWKKVLP ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 207 MET 2 208 PRO 3 209 GLY 4 210 SER 5 211 LEU 6 212 SER 7 213 GLY 8 214 ILE 9 215 ILE 10 216 ILE 11 217 TYR 12 218 VAL 13 219 THR 14 220 VAL 15 221 ALA 16 222 ALA 17 223 VAL 18 224 VAL 19 225 LEU 20 226 ILE 21 227 VAL 22 228 ALA 23 229 VAL 24 230 PHE 25 231 VAL 26 232 CYS 27 233 LYS 28 234 SER 29 235 LEU 30 236 LEU 31 237 TRP 32 238 LYS 33 239 LYS 34 240 VAL 35 241 LEU 36 242 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 'TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'recombinant technology' . . . 'BL21 (DE3)' pMM-LR6 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type bicelle _Details ; 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 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM '[U-13C; U-15N; 85%-2H]' DMPC 50 mM 'natural abundance' DHPC 100 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type bicelle _Details ; 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 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM '[U-13C; U-15N]' DMPC 50 mM '[acyl chain U-2H]' DHPC 100 mM '[acyl chain U-2H]' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type bicelle _Details ; 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 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM '[15%-13C; U-15N; H-2H]' DMPC 50 mM '[acyl chain U-2H]' DHPC 100 mM '[acyl chain U-2H]' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'cryogenic probe' save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 750 _Details 'cryogenic probe' save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details 'cryogenic probe' save_ ############################# # NMR applied experiments # ############################# save_TROSY_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'TROSY HSQC' _Sample_label $sample_1 save_ save_TROSY_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'TROSY HNCA' _Sample_label $sample_1 save_ save_TROSY_HNCOCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'TROSY HNCOCA' _Sample_label $sample_1 save_ save_TROSY_HNCACO_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'TROSY HNCACO' _Sample_label $sample_1 save_ save_TROSY_HNCO_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'TROSY HNCO' _Sample_label $sample_1 save_ save_3D_15N_NOE-TROSY-HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOE-TROSY-HSQC' _Sample_label $sample_1 save_ save_3D_15N_NOE-TROSY-HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOE-TROSY-HSQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_3D_13C_NOE-HSQC_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C NOE-HSQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_3 save_ save_3D_15N_NOE-TROSY-HSQC_11 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOE-TROSY-HSQC' _Sample_label $sample_3 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 7 . pH pressure 1 . atm temperature 303 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label 'TROSY HSQC' 'TROSY HNCA' 'TROSY HNCOCA' 'TROSY HNCACO' 'TROSY HNCO' '3D 15N NOE-TROSY-HSQC' '2D 1H-13C HSQC' '3D 13C NOE-HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 208 2 PRO C C 177.99 0.030 1 2 208 2 PRO CA C 62.77 0.050 1 3 209 3 GLY H H 8.47 0.002 1 4 209 3 GLY C C 178.70 0.030 1 5 209 3 GLY CA C 44.55 0.050 1 6 209 3 GLY N N 108.30 0.020 1 7 210 4 SER H H 8.24 0.002 1 8 210 4 SER C C 174.37 0.030 1 9 210 4 SER CA C 57.36 0.050 1 10 210 4 SER N N 115.76 0.020 1 11 211 5 LEU H H 8.69 0.002 1 12 211 5 LEU C C 177.09 0.030 1 13 211 5 LEU CA C 56.02 0.050 1 14 211 5 LEU N N 124.47 0.020 1 15 212 6 SER H H 8.25 0.002 1 16 212 6 SER C C 175.18 0.030 1 17 212 6 SER CA C 60.51 0.050 1 18 212 6 SER N N 114.79 0.020 1 19 213 7 GLY H H 8.07 0.002 1 20 213 7 GLY C C 174.44 0.030 1 21 213 7 GLY CA C 46.24 0.050 1 22 213 7 GLY N N 109.56 0.020 1 23 214 8 ILE H H 7.86 0.002 1 24 214 8 ILE C C 176.64 0.030 1 25 214 8 ILE CA C 63.97 0.050 1 26 214 8 ILE N N 120.11 0.020 1 27 215 9 ILE H H 7.97 0.002 1 28 215 9 ILE C C 178.29 0.030 1 29 215 9 ILE CA C 64.50 0.050 1 30 215 9 ILE N N 119.15 0.020 1 31 216 10 ILE H H 8.14 0.002 1 32 216 10 ILE C C 176.73 0.030 1 33 216 10 ILE CA C 64.64 0.050 1 34 216 10 ILE N N 122.73 0.020 1 35 217 11 TYR H H 8.11 0.002 1 36 217 11 TYR C C 177.75 0.030 1 37 217 11 TYR CA C 60.79 0.050 1 38 217 11 TYR N N 119.24 0.020 1 39 218 12 VAL H H 8.43 0.002 1 40 218 12 VAL C C 176.24 0.030 1 41 218 12 VAL CA C 65.91 0.050 1 42 218 12 VAL N N 116.82 0.020 1 43 219 13 THR H H 7.97 0.002 1 44 219 13 THR C C 175.63 0.030 1 45 219 13 THR CA C 67.64 0.050 1 46 219 13 THR N N 117.11 0.020 1 47 220 14 VAL H H 8.30 0.002 1 48 220 14 VAL C C 176.58 0.030 1 49 220 14 VAL CA C 66.44 0.050 1 50 220 14 VAL N N 120.02 0.020 1 51 221 15 ALA H H 8.15 0.002 1 52 221 15 ALA C C 177.69 0.030 1 53 221 15 ALA CA C 54.61 0.050 1 54 221 15 ALA N N 120.40 0.020 1 55 222 16 ALA H H 8.35 0.002 1 56 222 16 ALA C C 178.25 0.030 1 57 222 16 ALA CA C 54.93 0.050 1 58 222 16 ALA N N 118.47 0.020 1 59 223 17 VAL H H 8.05 0.002 1 60 223 17 VAL C C 176.80 0.030 1 61 223 17 VAL CA C 66.42 0.050 1 62 223 17 VAL N N 116.73 0.020 1 63 224 18 VAL H H 8.24 0.002 1 64 224 18 VAL C C 176.55 0.030 1 65 224 18 VAL CA C 66.58 0.050 1 66 224 18 VAL N N 118.66 0.020 1 67 225 19 LEU H H 8.17 0.002 1 68 225 19 LEU C C 177.46 0.030 1 69 225 19 LEU CA C 57.61 0.050 1 70 225 19 LEU N N 119.15 0.020 1 71 226 20 ILE H H 8.23 0.002 1 72 226 20 ILE C C 177.20 0.030 1 73 226 20 ILE CA C 64.82 0.050 1 74 226 20 ILE N N 118.57 0.020 1 75 227 21 VAL H H 8.33 0.002 1 76 227 21 VAL C C 176.90 0.030 1 77 227 21 VAL CA C 66.54 0.050 1 78 227 21 VAL N N 119.34 0.020 1 79 228 22 ALA H H 8.69 0.002 1 80 228 22 ALA C C 178.97 0.030 1 81 228 22 ALA CA C 55.07 0.050 1 82 228 22 ALA N N 121.28 0.020 1 83 229 23 VAL H H 8.38 0.002 1 84 229 23 VAL C C 176.42 0.030 1 85 229 23 VAL CA C 66.42 0.050 1 86 229 23 VAL N N 118.28 0.020 1 87 230 24 PHE H H 8.05 0.002 1 88 230 24 PHE C C 178.13 0.030 1 89 230 24 PHE CA C 61.53 0.050 1 90 230 24 PHE N N 119.15 0.020 1 91 231 25 VAL H H 8.85 0.002 1 92 231 25 VAL C C 177.21 0.030 1 93 231 25 VAL CA C 65.91 0.050 1 94 231 25 VAL N N 120.50 0.020 1 95 232 26 CYS H H 8.25 0.002 1 96 232 26 CYS C C 175.71 0.030 1 97 232 26 CYS CA C 63.54 0.050 1 98 232 26 CYS N N 117.69 0.020 1 99 233 27 LYS H H 8.30 0.002 1 100 233 27 LYS C C 177.14 0.030 1 101 233 27 LYS CA C 58.46 0.050 1 102 233 27 LYS N N 118.86 0.020 1 103 234 28 SER H H 7.72 0.002 1 104 234 28 SER C C 174.70 0.030 1 105 234 28 SER CA C 60.51 0.050 1 106 234 28 SER N N 113.43 0.020 1 107 235 29 LEU H H 7.67 0.002 1 108 235 29 LEU C C 177.16 0.030 1 109 235 29 LEU CA C 55.30 0.050 1 110 235 29 LEU N N 119.05 0.020 1 111 236 30 LEU H H 7.71 0.002 1 112 236 30 LEU C C 176.73 0.030 1 113 236 30 LEU CA C 55.56 0.050 1 114 236 30 LEU N N 117.69 0.020 1 115 237 31 TRP H H 7.71 0.002 1 116 237 31 TRP C C 175.52 0.030 1 117 237 31 TRP CA C 57.29 0.050 1 118 237 31 TRP N N 119.53 0.020 1 119 238 32 LYS H H 7.63 0.002 1 120 238 32 LYS C C 175.76 0.030 1 121 238 32 LYS CA C 55.74 0.050 1 122 238 32 LYS N N 120.60 0.020 1 123 239 33 LYS H H 7.94 0.002 1 124 239 33 LYS C C 175.71 0.030 1 125 239 33 LYS CA C 55.60 0.050 1 126 239 33 LYS N N 121.37 0.020 1 127 240 34 VAL H H 7.90 0.002 1 128 240 34 VAL C C 174.70 0.030 1 129 240 34 VAL CA C 61.48 0.050 1 130 240 34 VAL N N 120.69 0.020 1 131 241 35 LEU H H 7.91 0.002 1 132 241 35 LEU CA C 51.78 0.050 1 133 241 35 LEU N N 126.21 0.020 1 stop_ save_