data_17247 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR Structure of xenopus Fn14 ; _BMRB_accession_number 17247 _BMRB_flat_file_name bmr17247.str _Entry_type original _Submission_date 2010-10-11 _Accession_date 2010-10-11 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'solution NMR structure of xenopus Fn14 CRD' 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" 193 "15N chemical shifts" 36 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 xeFn14 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label xeFn14 $xeFn14 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_xeFn14 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common xeFn14 _Molecular_mass 5682.339 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 66 _Mol_residue_sequence ; SQGECPEGRAYSQDLGKCME CSVCKNSEKSDFCQNCPSKT EQPDFPWIWVEQKLISEEDL HHHHHH ; loop_ _Residue_seq_code _Residue_label 1 SER 2 GLN 3 GLY 4 GLU 5 CYS 6 PRO 7 GLU 8 GLY 9 ARG 10 ALA 11 TYR 12 SER 13 GLN 14 ASP 15 LEU 16 GLY 17 LYS 18 CYS 19 MET 20 GLU 21 CYS 22 SER 23 VAL 24 CYS 25 LYS 26 ASN 27 SER 28 GLU 29 LYS 30 SER 31 ASP 32 PHE 33 CYS 34 GLN 35 ASN 36 CYS 37 PRO 38 SER 39 LYS 40 THR 41 GLU 42 GLN 43 PRO 44 ASP 45 PHE 46 PRO 47 TRP 48 ILE 49 TRP 50 VAL 51 GLU 52 GLN 53 LYS 54 LEU 55 ILE 56 SER 57 GLU 58 GLU 59 ASP 60 LEU 61 HIS 62 HIS 63 HIS 64 HIS 65 HIS 66 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 PDB 2KN0 "Solution Nmr Structure Of Xenopus Fn14" 100.00 66 100.00 100.00 2.31e-40 GB AAI69735 "Fn14 protein [Xenopus laevis]" 75.76 120 100.00 100.00 9.58e-30 GB AAI69737 "Fn14 protein [Xenopus laevis]" 75.76 120 100.00 100.00 9.58e-30 GB AAR21225 "Fn14 [Xenopus laevis]" 75.76 120 100.00 100.00 1.14e-29 REF NP_001083640 "tumor necrosis factor receptor superfamily, member 12A precursor [Xenopus laevis]" 75.76 120 100.00 100.00 1.14e-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 $xeFn14 'African clawed frog' 8355 Eukaryota Metazoa Xenopus laevis '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 $xeFn14 'recombinant technology' . Pichia Pastoris . N/A stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $xeFn14 . uM 500 700 '[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_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . 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 _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_ ####################### # 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 'methyl protons' ppm 0.0 internal direct . . . 1.000000000 TSP N 15 'methyl 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 xeFn14 _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 3 3 GLY H H 8.028 0.002 1 2 3 3 GLY HA2 H 3.567 0.002 2 3 3 3 GLY HA3 H 3.413 0.001 2 4 3 3 GLY N N 110.780 0.009 1 5 4 4 GLU H H 7.992 0.002 1 6 4 4 GLU HA H 4.169 0.003 1 7 4 4 GLU HB2 H 1.884 0.000 2 8 4 4 GLU HB3 H 1.794 0.000 2 9 4 4 GLU HG2 H 2.027 0.001 1 10 4 4 GLU HG3 H 2.027 0.001 1 11 4 4 GLU N N 119.948 0.037 1 12 5 5 CYS H H 8.458 0.003 1 13 5 5 CYS HA H 5.109 0.008 1 14 5 5 CYS HB2 H 2.657 0.002 2 15 5 5 CYS HB3 H 2.485 0.004 2 16 5 5 CYS N N 119.368 0.034 1 17 6 6 PRO HA H 4.419 0.005 1 18 6 6 PRO HD2 H 3.858 0.000 2 19 6 6 PRO HD3 H 3.149 0.001 2 20 7 7 GLU H H 8.291 0.003 1 21 7 7 GLU HA H 3.987 0.003 1 22 7 7 GLU HB2 H 1.848 0.000 2 23 7 7 GLU HG2 H 2.197 0.004 1 24 7 7 GLU HG3 H 2.197 0.004 1 25 7 7 GLU N N 119.412 0.040 1 26 8 8 GLY H H 8.876 0.003 1 27 8 8 GLY HA2 H 4.261 0.010 2 28 8 8 GLY HA3 H 3.652 0.001 2 29 8 8 GLY N N 113.611 0.627 1 30 9 9 ARG H H 8.195 0.020 1 31 9 9 ARG HA H 5.305 0.004 1 32 9 9 ARG HB2 H 1.610 0.004 2 33 9 9 ARG HB3 H 1.367 0.001 2 34 9 9 ARG HD2 H 2.731 0.000 2 35 9 9 ARG HD3 H 2.638 0.016 2 36 9 9 ARG HG2 H 1.213 0.008 2 37 9 9 ARG N N 119.572 0.021 1 38 10 10 ALA H H 8.765 0.007 1 39 10 10 ALA HA H 4.507 0.002 1 40 10 10 ALA HB H 1.349 0.005 1 41 10 10 ALA N N 120.523 0.014 1 42 11 11 TYR H H 9.026 0.005 1 43 11 11 TYR HA H 3.843 0.002 1 44 11 11 TYR HB2 H 2.887 0.002 2 45 11 11 TYR HB3 H 2.672 0.007 2 46 11 11 TYR HD1 H 6.648 0.004 1 47 11 11 TYR HD2 H 6.648 0.004 1 48 11 11 TYR HE1 H 6.457 0.001 1 49 11 11 TYR HE2 H 6.457 0.001 1 50 11 11 TYR N N 123.732 0.010 1 51 12 12 SER H H 7.473 0.003 1 52 12 12 SER HA H 4.649 0.005 1 53 12 12 SER HB2 H 3.646 0.002 2 54 12 12 SER HB3 H 3.588 0.001 2 55 12 12 SER N N 121.259 0.015 1 56 13 13 GLN H H 8.660 0.004 1 57 13 13 GLN HA H 3.937 0.001 1 58 13 13 GLN HB2 H 2.069 0.004 1 59 13 13 GLN HB3 H 2.069 0.004 1 60 13 13 GLN HG2 H 2.459 0.006 1 61 13 13 GLN HG3 H 2.459 0.006 1 62 13 13 GLN N N 131.258 0.008 1 63 14 14 ASP H H 9.782 0.004 1 64 14 14 ASP HA H 4.216 0.002 1 65 14 14 ASP HB2 H 2.422 0.002 1 66 14 14 ASP HB3 H 2.422 0.002 1 67 14 14 ASP N N 121.230 0.012 1 68 15 15 LEU H H 7.718 0.003 1 69 15 15 LEU HA H 4.243 0.001 1 70 15 15 LEU HB2 H 1.294 0.005 2 71 15 15 LEU HB3 H 1.571 0.008 2 72 15 15 LEU HD1 H 0.885 0.000 2 73 15 15 LEU HD2 H 0.739 0.006 2 74 15 15 LEU N N 115.477 0.008 1 75 16 16 GLY H H 8.072 0.056 1 76 16 16 GLY HA2 H 3.741 0.000 2 77 16 16 GLY HA3 H 3.630 0.000 2 78 16 16 GLY N N 111.342 0.014 1 79 17 17 LYS H H 6.736 0.004 1 80 17 17 LYS HA H 4.560 0.002 1 81 17 17 LYS HB2 H 1.731 0.004 2 82 17 17 LYS HB3 H 1.476 0.002 2 83 17 17 LYS HG2 H 0.928 0.000 2 84 17 17 LYS HG3 H 0.791 0.006 2 85 17 17 LYS N N 111.749 0.029 1 86 18 18 CYS H H 8.787 0.001 1 87 18 18 CYS HA H 4.490 0.005 1 88 18 18 CYS HB2 H 3.032 0.002 2 89 18 18 CYS HB3 H 2.345 0.003 2 90 18 18 CYS N N 118.891 0.016 1 91 19 19 MET H H 8.668 0.009 1 92 19 19 MET HA H 4.543 0.003 1 93 19 19 MET HB2 H 0.871 0.007 2 94 19 19 MET HB3 H 0.123 0.006 2 95 19 19 MET HG2 H 1.766 0.005 2 96 19 19 MET HG3 H 1.610 0.005 2 97 19 19 MET N N 124.226 0.015 1 98 20 20 GLU H H 8.482 0.001 1 99 20 20 GLU HA H 4.063 0.006 1 100 20 20 GLU HB2 H 1.910 0.007 1 101 20 20 GLU HB3 H 1.910 0.007 1 102 20 20 GLU HG2 H 2.183 0.001 1 103 20 20 GLU HG3 H 2.183 0.001 1 104 20 20 GLU N N 119.707 0.010 1 105 21 21 CYS H H 8.675 0.003 1 106 21 21 CYS HA H 4.710 0.004 1 107 21 21 CYS HB2 H 3.059 0.001 2 108 21 21 CYS HB3 H 2.782 0.006 2 109 21 21 CYS N N 121.558 0.020 1 110 23 23 VAL H H 7.280 0.003 1 111 23 23 VAL HA H 4.072 0.002 1 112 23 23 VAL HB H 2.420 0.003 1 113 23 23 VAL HG1 H 1.135 0.005 2 114 23 23 VAL HG2 H 1.007 0.004 2 115 23 23 VAL N N 118.261 0.010 1 116 24 24 CYS H H 7.767 0.002 1 117 24 24 CYS HA H 4.180 0.000 1 118 24 24 CYS HB2 H 2.978 0.001 1 119 24 24 CYS HB3 H 2.978 0.001 1 120 24 24 CYS N N 119.304 0.017 1 121 28 28 GLU HG2 H 2.117 0.000 1 122 28 28 GLU HG3 H 2.117 0.000 1 123 29 29 LYS H H 8.202 0.004 1 124 29 29 LYS HA H 4.139 0.002 1 125 29 29 LYS HB2 H 1.739 0.001 2 126 29 29 LYS HB3 H 1.583 0.007 2 127 29 29 LYS HG2 H 1.262 0.005 1 128 29 29 LYS HG3 H 1.262 0.005 1 129 29 29 LYS N N 120.600 0.034 1 130 30 30 SER H H 7.536 0.003 1 131 30 30 SER HA H 4.281 0.002 1 132 30 30 SER HB2 H 3.636 0.002 2 133 30 30 SER HB3 H 3.342 0.004 2 134 30 30 SER N N 117.040 0.033 1 135 31 31 ASP H H 9.097 0.002 1 136 31 31 ASP HA H 4.101 0.004 1 137 31 31 ASP HB2 H 2.807 0.003 1 138 31 31 ASP HB3 H 2.807 0.003 1 139 31 31 ASP N N 126.257 0.013 1 140 32 32 PHE H H 8.631 0.003 1 141 32 32 PHE HA H 4.373 0.003 1 142 32 32 PHE HB2 H 2.778 0.006 2 143 32 32 PHE HB3 H 2.420 0.003 2 144 32 32 PHE HD1 H 6.908 0.002 1 145 32 32 PHE HD2 H 6.908 0.002 1 146 32 32 PHE HE1 H 7.291 0.004 1 147 32 32 PHE HE2 H 7.291 0.004 1 148 32 32 PHE HZ H 7.017 0.001 1 149 32 32 PHE N N 118.713 0.019 1 150 33 33 CYS H H 6.822 0.003 1 151 33 33 CYS HA H 3.919 0.004 1 152 33 33 CYS HB2 H 2.856 0.004 2 153 33 33 CYS HB3 H 2.577 0.002 2 154 33 33 CYS N N 118.803 0.016 1 155 34 34 GLN H H 7.875 0.003 1 156 34 34 GLN HA H 4.042 0.002 1 157 34 34 GLN HB2 H 1.979 0.002 1 158 34 34 GLN HB3 H 1.979 0.002 1 159 34 34 GLN HE21 H 7.404 0.000 1 160 34 34 GLN HE22 H 7.404 0.000 1 161 34 34 GLN HG2 H 2.291 0.002 1 162 34 34 GLN HG3 H 2.291 0.002 1 163 34 34 GLN N N 119.009 0.025 1 164 35 35 ASN H H 7.654 0.006 1 165 35 35 ASN HA H 4.936 0.001 1 166 35 35 ASN HB2 H 3.112 0.004 2 167 35 35 ASN HB3 H 2.627 0.006 2 168 35 35 ASN N N 115.831 0.019 1 169 36 36 CYS H H 7.218 0.003 1 170 36 36 CYS HA H 4.819 0.001 1 171 36 36 CYS HB2 H 3.090 0.003 2 172 36 36 CYS HB3 H 3.013 0.008 2 173 36 36 CYS N N 120.323 0.013 1 174 37 37 PRO HD2 H 3.803 0.001 2 175 37 37 PRO HD3 H 3.625 0.001 2 176 39 39 LYS HA H 4.288 0.000 1 177 40 40 THR H H 8.088 0.003 1 178 40 40 THR HA H 4.173 0.002 1 179 40 40 THR HB H 4.046 0.000 1 180 40 40 THR HG2 H 1.053 0.002 1 181 40 40 THR N N 115.451 0.028 1 182 42 42 GLN H H 8.280 0.001 1 183 42 42 GLN HA H 4.497 0.002 1 184 42 42 GLN HB2 H 1.967 0.000 2 185 42 42 GLN HB3 H 1.802 0.000 2 186 42 42 GLN HG2 H 2.236 0.000 1 187 42 42 GLN HG3 H 2.236 0.000 1 188 42 42 GLN N N 122.206 0.003 1 189 43 43 PRO HD2 H 3.586 0.000 2 190 43 43 PRO HD3 H 3.508 0.000 2 191 44 44 ASP H H 8.200 0.009 1 192 44 44 ASP HA H 4.342 0.008 1 193 44 44 ASP HB2 H 2.365 0.005 1 194 44 44 ASP HB3 H 2.365 0.005 1 195 44 44 ASP N N 119.590 0.030 1 196 45 45 PHE H H 7.773 0.002 1 197 45 45 PHE HA H 4.559 0.004 1 198 45 45 PHE HB2 H 2.570 0.000 1 199 45 45 PHE HB3 H 2.570 0.000 1 200 45 45 PHE HD1 H 7.026 0.000 1 201 45 45 PHE HD2 H 7.026 0.000 1 202 45 45 PHE N N 120.327 0.034 1 203 46 46 PRO HA H 4.221 0.001 1 204 46 46 PRO HD2 H 3.470 0.000 2 205 46 46 PRO HD3 H 3.124 0.000 2 206 47 47 TRP H H 7.630 0.002 1 207 47 47 TRP HA H 4.508 0.005 1 208 47 47 TRP HB2 H 3.062 0.002 1 209 47 47 TRP HB3 H 3.062 0.002 1 210 47 47 TRP N N 119.972 0.026 1 211 48 48 ILE H H 7.544 0.002 1 212 48 48 ILE HA H 3.953 0.001 1 213 48 48 ILE HB H 1.548 0.005 1 214 48 48 ILE HD1 H 0.776 0.127 1 215 48 48 ILE HG12 H 0.605 0.001 1 216 48 48 ILE HG13 H 0.605 0.001 1 217 48 48 ILE N N 121.765 0.025 1 218 49 49 TRP H H 7.887 0.008 1 219 49 49 TRP HA H 4.478 0.004 1 220 49 49 TRP HB2 H 3.112 0.006 2 221 49 49 TRP HB3 H 3.026 0.005 2 222 49 49 TRP HE3 H 7.420 0.002 1 223 49 49 TRP N N 124.602 0.017 1 224 50 50 VAL H H 7.657 0.004 1 225 50 50 VAL HA H 3.823 0.005 1 226 50 50 VAL HB H 1.813 0.002 1 227 50 50 VAL HG1 H 0.722 0.008 1 228 50 50 VAL HG2 H 0.722 0.008 1 229 50 50 VAL N N 122.559 0.036 1 stop_ save_