data_17237 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of hFn14 ; _BMRB_accession_number 17237 _BMRB_flat_file_name bmr17237.str _Entry_type original _Submission_date 2010-10-05 _Accession_date 2010-10-05 _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 Pellegrini M. . . 2 Willen L. . . 3 Perroud M. . . 4 Krushinskie D. . . 5 Strauch K. . . 6 Cuervo H. . . 7 Sun Y. . . 8 Day E. S. . 9 Schneider P. . . 10 Zheng T. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 163 "15N chemical shifts" 33 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-06-04 original author . stop_ _Original_release_date 2013-06-04 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of the extracellular domains of human and Xenopus Fn14: implications in the evolution of TWEAK and Fn14 interactions.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23438059 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pellegrini Maria . . 2 Willen Laure . . 3 Perroud Mai . . 4 Krushinskie Dennis . . 5 Strauch Kathy . . 6 Cuervo Hernan . . 7 Day Eric S. . 8 Schneider Pascal . . 9 Zheng Timothy S. . stop_ _Journal_abbreviation 'FEBS J.' _Journal_name_full 'The FEBS journal' _Journal_volume 280 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1818 _Page_last 1829 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name hFn14 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label hFn14 $Fn14 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Fn14 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Fn14 _Molecular_mass 5615.414 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 53 _Mol_residue_sequence ; EQAPGTAPCSRGSSWSADLD KCMDCASCRARPHSDFCLGC AAAPPAPFRLLWP ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 GLN 3 ALA 4 PRO 5 GLY 6 THR 7 ALA 8 PRO 9 CYS 10 SER 11 ARG 12 GLY 13 SER 14 SER 15 TRP 16 SER 17 ALA 18 ASP 19 LEU 20 ASP 21 LYS 22 CYS 23 MET 24 ASP 25 CYS 26 ALA 27 SER 28 CYS 29 ARG 30 ALA 31 ARG 32 PRO 33 HIS 34 SER 35 ASP 36 PHE 37 CYS 38 LEU 39 GLY 40 CYS 41 ALA 42 ALA 43 ALA 44 PRO 45 PRO 46 ALA 47 PRO 48 PHE 49 ARG 50 LEU 51 LEU 52 TRP 53 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-13 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 11346 "CRD domain, UNP residues 28-70" 81.13 50 100.00 100.00 1.54e-20 PDB 2EQP "Solution Structure Of The Stn_tnfrsf12a_tnfr Domain Of Tumor Necrosis Factor Receptor Superfamily Member 12a Precursor" 81.13 50 100.00 100.00 1.54e-20 PDB 2KMZ "Nmr Structure Of Hfn14" 100.00 53 100.00 100.00 3.85e-28 PDB 2RPJ "Solution Structure Of Fn14 Crd Domain" 81.13 50 100.00 100.00 1.54e-20 DBJ BAA94792 "type I transmenmbrane protein [Homo sapiens]" 100.00 129 100.00 100.00 7.05e-29 DBJ BAJ20302 "tumor necrosis factor receptor superfamily, member 12A [synthetic construct]" 100.00 129 100.00 100.00 7.05e-29 GB AAF69108 "type I transmembrane protein Fn14 [Homo sapiens]" 100.00 129 100.00 100.00 7.05e-29 GB AAH02718 "Tumor necrosis factor receptor superfamily, member 12A [Homo sapiens]" 100.00 129 100.00 100.00 7.05e-29 GB ABM83894 "tumor necrosis factor receptor superfamily, member 12A [synthetic construct]" 100.00 129 100.00 100.00 7.05e-29 GB ABM87215 "tumor necrosis factor receptor superfamily, member 12A [synthetic construct]" 100.00 129 100.00 100.00 7.05e-29 GB EAW85429 "tumor necrosis factor receptor superfamily, member 12A, isoform CRA_b [Homo sapiens]" 100.00 129 100.00 100.00 7.05e-29 REF NP_057723 "tumor necrosis factor receptor superfamily member 12A precursor [Homo sapiens]" 100.00 129 100.00 100.00 7.05e-29 REF XP_001089176 "PREDICTED: tumor necrosis factor receptor superfamily member 12A isoform 2 [Macaca mulatta]" 100.00 129 100.00 100.00 7.05e-29 REF XP_001165479 "PREDICTED: tumor necrosis factor receptor superfamily member 12A [Pan troglodytes]" 100.00 129 100.00 100.00 7.05e-29 REF XP_002826080 "PREDICTED: tumor necrosis factor receptor superfamily member 12A [Pongo abelii]" 100.00 129 100.00 100.00 7.44e-29 REF XP_003269240 "PREDICTED: tumor necrosis factor receptor superfamily member 12A isoform X2 [Nomascus leucogenys]" 100.00 129 100.00 100.00 6.33e-29 SP Q9NP84 "RecName: Full=Tumor necrosis factor receptor superfamily member 12A; AltName: Full=Fibroblast growth factor-inducible immediate" 100.00 129 100.00 100.00 7.05e-29 stop_ 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 $Fn14 Human 9606 Eukaryota Metazoa Homo sapiens 'TNFRSF12A, FN14' 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 $Fn14 'recombinant technology' . Pichia Pastoris . N/A stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details 'pH 7.4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Fn14 700 uM '[U-99% 15N]' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 137 mM 'natural abundance' 'potassium chloride' 2.7 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'pH 7.4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Fn14 700 uM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 137 mM 'natural abundance' 'potassium chloride' 2.7 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.11 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength '600 MHz' _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-15N_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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' 140 . mM pH 7.4 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 TSP H 1 protons ppm 0.0 internal direct . . . 1 TSP N 15 protons ppm 0.0 internal indirect . . . 0.101329118 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '3D 1H-15N NOESY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name hFn14 _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 5 5 GLY H H 8.387 0.002 1 2 5 5 GLY HA2 H 3.753 0.000 1 3 5 5 GLY HA3 H 3.753 0.000 1 4 5 5 GLY N N 109.547 0.018 1 5 6 6 THR H H 7.596 0.001 1 6 6 6 THR HA H 3.972 0.005 1 7 6 6 THR HB H 3.796 0.012 1 8 6 6 THR HG2 H 0.913 0.000 1 9 6 6 THR N N 113.035 0.026 1 10 7 7 ALA H H 7.819 0.003 1 11 7 7 ALA HA H 4.376 0.002 1 12 7 7 ALA HB H 1.110 0.011 1 13 7 7 ALA N N 127.585 0.030 1 14 8 8 PRO HA H 4.268 0.000 1 15 8 8 PRO HD2 H 3.502 0.000 1 16 8 8 PRO HD3 H 3.502 0.000 1 17 9 9 CYS H H 8.193 0.003 1 18 9 9 CYS HA H 4.847 0.008 1 19 9 9 CYS HB2 H 3.236 0.005 2 20 9 9 CYS HB3 H 2.472 0.007 2 21 9 9 CYS N N 117.923 0.022 1 22 13 13 SER H H 8.334 0.001 1 23 13 13 SER HA H 5.423 0.002 1 24 13 13 SER HB2 H 3.523 0.000 2 25 13 13 SER HB3 H 3.469 0.000 2 26 13 13 SER N N 117.003 0.007 1 27 14 14 SER H H 8.760 0.003 1 28 14 14 SER HA H 4.549 0.005 1 29 14 14 SER HB2 H 3.672 0.003 2 30 14 14 SER HB3 H 3.533 0.000 2 31 14 14 SER N N 113.766 0.018 1 32 15 15 TRP H H 8.770 0.003 1 33 15 15 TRP HA H 4.127 0.003 1 34 15 15 TRP HB2 H 3.218 0.002 2 35 15 15 TRP HB3 H 3.010 0.006 2 36 15 15 TRP HD1 H 6.879 0.007 1 37 15 15 TRP HE1 H 10.107 0.103 1 38 15 15 TRP HE3 H 7.462 0.003 1 39 15 15 TRP HZ2 H 7.231 0.003 1 40 15 15 TRP N N 128.367 0.025 1 41 16 16 SER H H 7.642 0.027 1 42 16 16 SER HA H 4.585 0.002 1 43 16 16 SER HB2 H 3.661 0.005 2 44 16 16 SER HB3 H 3.511 0.006 2 45 16 16 SER N N 122.520 0.024 1 46 17 17 ALA H H 8.347 0.005 1 47 17 17 ALA HA H 4.163 0.004 1 48 17 17 ALA HB H 1.464 0.006 1 49 17 17 ALA N N 133.697 0.032 1 50 18 18 ASP H H 9.896 0.004 1 51 18 18 ASP HA H 4.203 0.010 1 52 18 18 ASP HB2 H 2.420 0.010 1 53 18 18 ASP HB3 H 2.420 0.010 1 54 18 18 ASP N N 120.485 0.015 1 55 19 19 LEU H H 7.472 0.001 1 56 19 19 LEU HA H 4.188 0.009 1 57 19 19 LEU HB2 H 1.287 0.005 2 58 19 19 LEU HB3 H 1.149 0.011 2 59 19 19 LEU N N 115.936 0.020 1 60 20 20 ASP H H 7.823 0.004 1 61 20 20 ASP HA H 3.954 0.003 1 62 20 20 ASP HB2 H 3.032 0.003 2 63 20 20 ASP HB3 H 2.168 0.009 2 64 20 20 ASP N N 123.118 0.027 1 65 21 21 LYS H H 6.378 0.002 1 66 21 21 LYS HA H 4.032 0.038 1 67 21 21 LYS HB2 H 1.640 0.007 2 68 21 21 LYS HB3 H 1.355 0.019 2 69 21 21 LYS HE2 H 2.987 0.000 1 70 21 21 LYS HE3 H 2.987 0.000 1 71 21 21 LYS HG2 H 0.900 0.000 2 72 21 21 LYS HG3 H 0.629 0.011 2 73 21 21 LYS N N 110.105 0.024 1 74 22 22 CYS H H 8.562 0.006 1 75 22 22 CYS HA H 4.426 0.052 1 76 22 22 CYS HB2 H 2.808 0.008 2 77 22 22 CYS HB3 H 2.594 0.008 2 78 22 22 CYS N N 119.303 0.018 1 79 23 23 MET H H 8.384 0.002 1 80 23 23 MET HA H 4.467 0.047 1 81 23 23 MET HB2 H -0.053 0.009 1 82 23 23 MET HB3 H -0.053 0.009 1 83 23 23 MET HE H 1.729 0.000 1 84 23 23 MET HG2 H 1.663 0.023 2 85 23 23 MET HG3 H 0.521 0.009 2 86 23 23 MET N N 122.445 0.025 1 87 24 24 ASP H H 7.997 0.004 1 88 24 24 ASP HA H 4.319 0.006 1 89 24 24 ASP HB2 H 2.623 0.003 2 90 24 24 ASP HB3 H 2.490 0.021 2 91 24 24 ASP N N 120.230 0.016 1 92 25 25 CYS H H 8.857 0.002 1 93 25 25 CYS HA H 4.650 0.002 1 94 25 25 CYS HB2 H 3.039 0.004 2 95 25 25 CYS HB3 H 2.831 0.005 2 96 25 25 CYS N N 124.275 0.017 1 97 26 26 ALA H H 9.149 0.004 1 98 26 26 ALA HA H 4.041 0.006 1 99 26 26 ALA HB H 1.372 0.009 1 100 26 26 ALA N N 125.697 0.037 1 101 27 27 SER H H 7.654 0.008 1 102 27 27 SER HA H 4.277 0.007 1 103 27 27 SER HB2 H 4.117 0.009 2 104 27 27 SER HB3 H 3.996 0.002 2 105 27 27 SER N N 111.976 0.019 1 106 28 28 CYS H H 7.863 0.001 1 107 28 28 CYS HA H 4.049 0.005 1 108 28 28 CYS HB2 H 2.941 0.007 1 109 28 28 CYS HB3 H 2.941 0.007 1 110 28 28 CYS N N 119.484 0.016 1 111 29 29 ARG H H 7.161 0.001 1 112 29 29 ARG HA H 3.906 0.006 1 113 29 29 ARG HB2 H 1.770 0.010 1 114 29 29 ARG HB3 H 1.770 0.010 1 115 29 29 ARG HG2 H 1.628 0.000 2 116 29 29 ARG HG3 H 1.535 0.000 2 117 29 29 ARG N N 118.024 0.026 1 118 30 30 ALA HA H 4.281 0.000 1 119 30 30 ALA HB H 1.355 0.000 1 120 31 31 ARG H H 7.582 0.005 1 121 31 31 ARG HA H 4.719 0.012 1 122 31 31 ARG HB2 H 1.554 0.010 1 123 31 31 ARG HB3 H 1.554 0.010 1 124 31 31 ARG HD2 H 3.108 0.014 1 125 31 31 ARG HD3 H 3.108 0.014 1 126 31 31 ARG N N 116.425 0.017 1 127 32 32 PRO HA H 4.589 0.006 1 128 32 32 PRO HB2 H 1.558 0.000 1 129 32 32 PRO HB3 H 1.558 0.000 1 130 32 32 PRO HD2 H 3.429 0.000 1 131 32 32 PRO HD3 H 3.429 0.000 1 132 32 32 PRO HG2 H 1.558 0.000 1 133 32 32 PRO HG3 H 1.558 0.000 1 134 33 33 HIS H H 7.933 0.004 1 135 33 33 HIS HA H 4.417 0.004 1 136 33 33 HIS HB2 H 2.955 0.010 1 137 33 33 HIS HB3 H 2.955 0.010 1 138 33 33 HIS N N 115.767 0.016 1 139 34 34 SER H H 6.754 0.002 1 140 34 34 SER HA H 4.083 0.006 1 141 34 34 SER HB2 H 3.496 0.006 2 142 34 34 SER HB3 H 2.932 0.016 2 143 34 34 SER N N 116.122 0.019 1 144 35 35 ASP H H 9.380 0.004 1 145 35 35 ASP HA H 3.991 0.004 1 146 35 35 ASP HB2 H 2.870 0.000 1 147 35 35 ASP HB3 H 2.870 0.000 1 148 35 35 ASP N N 128.987 0.054 1 149 36 36 PHE H H 8.525 0.003 1 150 36 36 PHE HA H 4.408 0.004 1 151 36 36 PHE HB2 H 2.798 0.008 2 152 36 36 PHE HB3 H 2.360 0.006 2 153 36 36 PHE HD1 H 6.887 0.001 1 154 36 36 PHE HD2 H 6.887 0.001 1 155 36 36 PHE HE1 H 7.298 0.002 1 156 36 36 PHE HE2 H 7.298 0.002 1 157 36 36 PHE HZ H 7.043 0.002 1 158 36 36 PHE N N 118.319 0.018 1 159 37 37 CYS H H 7.219 0.006 1 160 37 37 CYS HA H 4.020 0.005 1 161 37 37 CYS HB2 H 2.897 0.005 2 162 37 37 CYS HB3 H 2.660 0.005 2 163 37 37 CYS N N 120.529 0.016 1 164 38 38 LEU H H 7.583 0.001 1 165 38 38 LEU HA H 4.091 0.010 1 166 38 38 LEU HB2 H 1.707 0.000 2 167 38 38 LEU HB3 H 1.588 0.000 2 168 38 38 LEU HD2 H 0.823 0.030 2 169 38 38 LEU N N 123.305 0.025 1 170 39 39 GLY H H 7.819 0.004 1 171 39 39 GLY HA2 H 4.087 0.020 2 172 39 39 GLY HA3 H 3.862 0.004 2 173 39 39 GLY N N 106.716 0.033 1 174 40 40 CYS H H 7.525 0.006 1 175 40 40 CYS HA H 4.461 0.004 1 176 40 40 CYS HB2 H 3.204 0.006 2 177 40 40 CYS HB3 H 3.070 0.008 2 178 40 40 CYS N N 119.062 0.019 1 179 41 41 ALA H H 7.767 0.006 1 180 41 41 ALA HA H 4.169 0.005 1 181 41 41 ALA HB H 1.338 0.018 1 182 41 41 ALA N N 123.176 0.012 1 183 47 47 PRO HA H 4.238 0.003 1 184 48 48 PHE H H 8.046 0.004 1 185 48 48 PHE HA H 4.423 0.010 1 186 48 48 PHE HB2 H 2.954 0.002 1 187 48 48 PHE HB3 H 2.954 0.002 1 188 48 48 PHE HD1 H 7.104 0.000 1 189 48 48 PHE HD2 H 7.104 0.000 1 190 48 48 PHE N N 119.947 0.005 1 191 52 52 TRP H H 7.938 0.004 1 192 52 52 TRP HA H 4.830 0.006 1 193 52 52 TRP HB2 H 3.188 0.007 2 194 52 52 TRP HB3 H 2.957 0.010 2 195 52 52 TRP HE3 H 7.518 0.000 1 196 52 52 TRP N N 121.930 0.018 1 stop_ save_