data_30799 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Transmembrane structure of TNFR1 ; _BMRB_accession_number 30799 _BMRB_flat_file_name bmr30799.str _Entry_type original _Submission_date 2020-09-22 _Accession_date 2020-09-22 _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 Zhao L. . . 2 Chou J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 26 "13C chemical shifts" 54 "15N chemical shifts" 26 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-09-28 original BMRB . stop_ _Original_release_date 2020-09-24 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The diversity and similarity of transmembrane trimerization of TNF receptors ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhao L. . . 2 Fu Q. . . 3 Pan L. . . 4 Piai A. . . 5 Chou J. . . stop_ _Journal_abbreviation 'To be published' _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Tumor necrosis factor receptor superfamily member 1A' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_1 $entity_1 unit_2 $entity_1 unit_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 3371.109 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; GTTVLLPLVIFFGLALLSLL FIGLAYRYQR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 209 GLY 2 210 THR 3 211 THR 4 212 VAL 5 213 LEU 6 214 LEU 7 215 PRO 8 216 LEU 9 217 VAL 10 218 ILE 11 219 PHE 12 220 PHE 13 221 GLY 14 222 LEU 15 223 ALA 16 224 LEU 17 225 LEU 18 226 SER 19 227 LEU 20 228 LEU 21 229 PHE 22 230 ILE 23 231 GLY 24 232 LEU 25 233 ALA 26 234 TYR 27 235 ARG 28 236 TYR 29 237 GLN 30 238 ARG 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 'TNFRSF1A, TNFAR, TNFR1' 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' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type bicelle _Details '0.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] Protein, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.7 mM '[U-100% 13C; U-100% 15N; U-80% 2H]' 'sodium phosphate' 20 mM 'natural abundance' DMPC 50 mM 'natural abundance' DHPC 100 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type bicelle _Details '0.7 mM [U-100% 13C; U-100% 15N] Protein, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.7 mM '[U-100% 13C; U-100% 15N]' 'sodium phosphate' 20 mM 'natural abundance' DMPC 50 mM 'natural abundance' DHPC 100 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type bicelle _Details ; 0.4 mM [U-100% 13C] Protein A, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 0.4 mM [U-100% 2H; U-100% 15N] Protein B, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'sodium phosphate' 20 mM 'natural abundance' DMPC 50 mM 'natural abundance' DHPC 100 mM 'natural abundance' $entity_1 0.4 mM '[U-100% 13C]' $entity_1 0.4 mM '[U-100% 2H; U-100% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address Bartels . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _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_3 _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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 750 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_HNCO_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACO_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACO' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_2 save_ save_3D_1H-15N_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_3 save_ save_3D_1H-13C_NOESY_FOR_METHYLS_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY FOR METHYLS' _Sample_label $sample_3 save_ save_2D_1H-13C_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 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 6.8 . 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 TMS C 13 nitrogen ppm 0 external indirect . . . . TMS H 1 protons ppm 0 external direct . . . 1.0 TMS N 15 'carbonyl carbon' ppm 0 external indirect . . . . 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 '3D HNCO' '3D HNCA' '3D HNCACO' '3D 1H-15N NOESY' '3D 1H-13C NOESY FOR METHYLS' '2D 1H-13C 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 unit_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 1 211 3 THR C C 177.19 0.030 1 2 211 3 THR CA C 61.38 0.050 1 3 212 4 VAL H H 8.11 0.002 1 4 212 4 VAL C C 177.70 0.030 1 5 212 4 VAL CA C 61.66 0.050 1 6 212 4 VAL N N 119.58 0.020 1 7 213 5 LEU H H 7.90 0.002 1 8 213 5 LEU C C 179.85 0.030 1 9 213 5 LEU CA C 56.18 0.050 1 10 213 5 LEU N N 120.40 0.020 1 11 214 6 LEU H H 8.27 0.002 1 12 214 6 LEU CA C 58.45 0.050 1 13 214 6 LEU N N 118.39 0.020 1 14 215 7 PRO C C 179.60 0.030 1 15 215 7 PRO CA C 65.08 0.050 1 16 216 8 LEU H H 7.36 0.002 1 17 216 8 LEU C C 180.34 0.030 1 18 216 8 LEU CA C 57.21 0.050 1 19 216 8 LEU N N 115.82 0.020 1 20 217 9 VAL H H 8.28 0.002 1 21 217 9 VAL C C 179.89 0.030 1 22 217 9 VAL CA C 65.70 0.050 1 23 217 9 VAL N N 119.30 0.020 1 24 218 10 ILE H H 8.09 0.002 1 25 218 10 ILE C C 179.31 0.030 1 26 218 10 ILE CA C 64.16 0.050 1 27 218 10 ILE N N 119.49 0.020 1 28 219 11 PHE H H 8.47 0.002 1 29 219 11 PHE C C 178.78 0.030 1 30 219 11 PHE CA C 60.75 0.050 1 31 219 11 PHE N N 119.39 0.020 1 32 220 12 PHE H H 8.68 0.002 1 33 220 12 PHE C C 179.72 0.030 1 34 220 12 PHE CA C 60.32 0.050 1 35 220 12 PHE N N 118.02 0.020 1 36 221 13 GLY H H 8.70 0.002 1 37 221 13 GLY C C 176.68 0.030 1 38 221 13 GLY CA C 46.35 0.050 1 39 221 13 GLY N N 107.47 0.020 1 40 222 14 LEU H H 8.45 0.002 1 41 222 14 LEU C C 181.68 0.030 1 42 222 14 LEU CA C 56.49 0.050 1 43 222 14 LEU N N 121.23 0.020 1 44 223 15 ALA H H 8.41 0.002 1 45 223 15 ALA C C 180.83 0.030 1 46 223 15 ALA CA C 54.19 0.050 1 47 223 15 ALA N N 124.44 0.020 1 48 224 16 LEU H H 8.16 0.002 1 49 224 16 LEU C C 180.44 0.030 1 50 224 16 LEU CA C 56.88 0.050 1 51 224 16 LEU N N 118.20 0.020 1 52 225 17 LEU H H 8.14 0.002 1 53 225 17 LEU C C 180.37 0.030 1 54 225 17 LEU CA C 56.81 0.050 1 55 225 17 LEU N N 118.20 0.020 1 56 226 18 SER H H 8.04 0.002 1 57 226 18 SER C C 177.49 0.030 1 58 226 18 SER CA C 62.47 0.050 1 59 226 18 SER N N 115.36 0.020 1 60 227 19 LEU H H 7.80 0.002 1 61 227 19 LEU C C 180.37 0.030 1 62 227 19 LEU CA C 56.73 0.050 1 63 227 19 LEU N N 121.87 0.020 1 64 228 20 LEU H H 8.00 0.002 1 65 228 20 LEU C C 180.05 0.030 1 66 228 20 LEU CA C 56.95 0.050 1 67 228 20 LEU N N 119.21 0.020 1 68 229 21 PHE H H 8.25 0.002 1 69 229 21 PHE C C 179.32 0.030 1 70 229 21 PHE CA C 60.42 0.050 1 71 229 21 PHE N N 117.84 0.020 1 72 230 22 ILE H H 8.36 0.002 1 73 230 22 ILE C C 179.70 0.030 1 74 230 22 ILE CA C 64.04 0.050 1 75 230 22 ILE N N 119.30 0.020 1 76 231 23 GLY H H 8.49 0.002 1 77 231 23 GLY C C 177.35 0.030 1 78 231 23 GLY CA C 46.45 0.050 1 79 231 23 GLY N N 107.20 0.020 1 80 232 24 LEU H H 8.34 0.002 1 81 232 24 LEU C C 180.45 0.030 1 82 232 24 LEU CA C 56.51 0.050 1 83 232 24 LEU N N 121.41 0.020 1 84 233 25 ALA H H 8.26 0.002 1 85 233 25 ALA C C 181.22 0.030 1 86 233 25 ALA CA C 53.86 0.050 1 87 233 25 ALA N N 121.60 0.020 1 88 234 26 TYR H H 8.18 0.002 1 89 234 26 TYR C C 179.41 0.030 1 90 234 26 TYR CA C 59.69 0.050 1 91 234 26 TYR N N 117.10 0.020 1 92 235 27 ARG H H 7.80 0.002 1 93 235 27 ARG C C 179.15 0.030 1 94 235 27 ARG CA C 56.07 0.050 1 95 235 27 ARG N N 118.11 0.020 1 96 236 28 TYR H H 7.83 0.002 1 97 236 28 TYR C C 177.39 0.030 1 98 236 28 TYR CA C 58.11 0.050 1 99 236 28 TYR N N 118.11 0.020 1 100 237 29 GLN H H 7.53 0.002 1 101 237 29 GLN C C 176.65 0.030 1 102 237 29 GLN CA C 54.73 0.050 1 103 237 29 GLN N N 120.31 0.020 1 104 238 30 ARG H H 7.64 0.002 1 105 238 30 ARG CA C 56.28 0.050 1 106 238 30 ARG N N 127.56 0.020 1 stop_ save_