data_27549 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H, 13C, and 15N Chemical Shift Assignments for TDP-43 RRM2 at 6M urea ; _BMRB_accession_number 27549 _BMRB_flat_file_name bmr27549.str _Entry_type original _Submission_date 2018-07-17 _Accession_date 2018-07-17 _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 Mackness Brian C. . 2 Morgan Brittany R. . 3 Deveau Laura M. . 4 Kathuria Sagar V. . 5 Tavella Davide . . 6 Massi Francesca . . 7 Zitzewitz Jill A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 58 "13C chemical shifts" 121 "15N chemical shifts" 58 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-11-15 original BMRB . stop_ _Original_release_date 2018-07-17 save_ ############################# # Citation for this entry # ############################# save_manuscript _Saveframe_category entry_citation _Citation_full . _Citation_title ; Characterization of TDP-43 RRM2 Partially Folded States and Their Significance to ALS Pathogenesis. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30309612 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tavella Davide . . 2 Zitzewitz Jill A. . 3 Massi Francesca . . stop_ _Journal_abbreviation 'Biophys. J.' _Journal_name_full 'Biophysical journal' _Journal_volume 115 _Journal_issue 9 _Journal_ISSN 1542-0086 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1673 _Page_last 1680 _Year 2018 _Details . loop_ _Keyword NMR TDP-43 intermediate 'partially folded states' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'TDP-43 RRM2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TDP-43 RRM2' $TDP-43_RRM2 stop_ _System_molecular_weight . _System_physical_state denatured _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TDP-43_RRM2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TDP-43_RRM2 _Molecular_mass 8506.6182 _Mol_thiol_state 'all free' loop_ _Biological_function 'gene transcription, splicing, mRNA processing, and mRNA stability.' stop_ _Details 'Data collected in 6M urea.' ############################## # Polymer residue sequence # ############################## _Residue_count 76 _Mol_residue_sequence ; GPLGSRKVFVGRCTEDMTED ELREFFSQYGDVMDVFIPKP FRAFAFVTFADDQIAQSLCG EDLIIKGISVHISNAE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 186 GLY 2 187 PRO 3 188 LEU 4 189 GLY 5 190 SER 6 191 ARG 7 192 LYS 8 193 VAL 9 194 PHE 10 195 VAL 11 196 GLY 12 197 ARG 13 198 CYS 14 199 THR 15 200 GLU 16 201 ASP 17 202 MET 18 203 THR 19 204 GLU 20 205 ASP 21 206 GLU 22 207 LEU 23 208 ARG 24 209 GLU 25 210 PHE 26 211 PHE 27 212 SER 28 213 GLN 29 214 TYR 30 215 GLY 31 216 ASP 32 217 VAL 33 218 MET 34 219 ASP 35 220 VAL 36 221 PHE 37 222 ILE 38 223 PRO 39 224 LYS 40 225 PRO 41 226 PHE 42 227 ARG 43 228 ALA 44 229 PHE 45 230 ALA 46 231 PHE 47 232 VAL 48 233 THR 49 234 PHE 50 235 ALA 51 236 ASP 52 237 ASP 53 238 GLN 54 239 ILE 55 240 ALA 56 241 GLN 57 242 SER 58 243 LEU 59 244 CYS 60 245 GLY 61 246 GLU 62 247 ASP 63 248 LEU 64 249 ILE 65 250 ILE 66 251 LYS 67 252 GLY 68 253 ILE 69 254 SER 70 255 VAL 71 256 HIS 72 257 ILE 73 258 SER 74 259 ASN 75 260 ALA 76 261 GLU 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 $TDP-43_RRM2 Human 9606 Eukaryota Metazoa Homo sapiens 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 $TDP-43_RRM2 'recombinant technology' . Escherichia coli . pGEX-6p1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; pH6.8 Urea added to populate the intermediate state ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling MOPS 20 mM 'natural abundance' 'potassium chloride' 25 mM 'natural abundance' beta-mercaptoethanol 1 mM 'natural abundance' $TDP-43_RRM2 .47 mM '[U-100% 13C; U-100% 15N]' urea 6 M 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 2.2 loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_NMRPipe _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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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_HN(CO)CA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CO)CA' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH pressure 1 . atm temperature 273 . 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 DSS C 13 'methyl protons' ppm 0.00 external indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 external direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 external 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 '2D 1H-15N HSQC' '3D HNCA' '3D HN(CO)CA' '3D CBCA(CO)NH' '3D HNCACB' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'TDP-43 RRM2' _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 1 190 5 SER H H 8.180 0.01 1 2 190 5 SER CA C 58.500 0.2 1 3 190 5 SER CB C 64.300 0.2 1 4 190 5 SER N N 115.400 0.2 1 5 191 6 ARG H H 8.400 0.01 1 6 191 6 ARG CA C 56.100 0.2 1 7 191 6 ARG CB C 33.200 0.2 1 8 191 6 ARG N N 122.900 0.2 1 9 192 7 LYS H H 8.450 0.01 1 10 192 7 LYS CA C 56.400 0.2 1 11 192 7 LYS CB C 33.300 0.2 1 12 192 7 LYS N N 123.500 0.2 1 13 193 8 VAL H H 8.170 0.01 1 14 193 8 VAL CA C 63.200 0.2 1 15 193 8 VAL CB C 33.100 0.2 1 16 193 8 VAL N N 121.50 0.2 1 17 194 9 PHE H H 8.310 0.01 1 18 194 9 PHE CA C 57.800 0.2 1 19 194 9 PHE CB C 41.700 0.2 1 20 194 9 PHE N N 121.100 0.2 1 21 195 10 VAL H H 8.100 0.01 1 22 195 10 VAL CA C 62.200 0.2 1 23 195 10 VAL CB C 32.900 0.2 1 24 195 10 VAL N N 119.300 0.2 1 25 196 11 GLY H H 8.020 0.01 1 26 196 11 GLY CA C 45.400 0.2 1 27 196 11 GLY N N 111.700 0.2 1 28 197 12 ARG H H 8.190 0.01 1 29 197 12 ARG CA C 56.000 0.2 1 30 197 12 ARG CB C 31.600 0.2 1 31 197 12 ARG N N 120.100 0.2 1 32 198 13 CYS CA C 55.700 0.2 1 33 198 13 CYS CB C 41.000 0.2 1 34 199 14 THR H H 8.320 0.01 1 35 199 14 THR CA C 62.900 0.2 1 36 199 14 THR CB C 69.400 0.2 1 37 199 14 THR N N 115.800 0.2 1 38 200 15 GLU H H 8.560 0.01 1 39 200 15 GLU CA C 58.000 0.2 1 40 200 15 GLU CB C 30.000 0.2 1 41 200 15 GLU N N 121.200 0.2 1 42 201 16 ASP H H 8.050 0.01 1 43 201 16 ASP CA C 54.400 0.2 1 44 201 16 ASP CB C 41.600 0.2 1 45 201 16 ASP N N 118.600 0.2 1 46 202 17 MET H H 7.770 0.01 1 47 202 17 MET CA C 56.300 0.2 1 48 202 17 MET CB C 34.500 0.2 1 49 202 17 MET N N 120.100 0.2 1 50 203 18 THR H H 8.750 0.01 1 51 203 18 THR CA C 61.400 0.2 1 52 203 18 THR CB C 70.800 0.2 1 53 203 18 THR N N 114.000 0.2 1 54 204 19 GLU H H 8.870 0.01 1 55 204 19 GLU CA C 59.600 0.2 1 56 204 19 GLU CB C 29.900 0.2 1 57 204 19 GLU N N 121.000 0.2 1 58 205 20 ASP H H 8.340 0.01 1 59 205 20 ASP CA C 57.000 0.2 1 60 205 20 ASP CB C 41.200 0.2 1 61 205 20 ASP N N 118.400 0.2 1 62 206 21 GLU H H 7.850 0.01 1 63 206 21 GLU CA C 58.700 0.2 1 64 206 21 GLU CB C 30.400 0.2 1 65 206 21 GLU N N 120.800 0.2 1 66 207 22 LEU H H 8.500 0.01 1 67 207 22 LEU CA C 57.500 0.2 1 68 207 22 LEU CB C 42.300 0.2 1 69 207 22 LEU N N 121.700 0.2 1 70 208 23 ARG CA C 58.800 0.2 1 71 208 23 ARG CB C 30.200 0.2 1 72 209 24 GLU H H 7.920 0.01 1 73 209 24 GLU CA C 58.500 0.2 1 74 209 24 GLU CB C 30.200 0.2 1 75 209 24 GLU N N 119.600 0.2 1 76 210 25 PHE H H 8.380 0.01 1 77 210 25 PHE CA C 60.400 0.2 1 78 210 25 PHE CB C 39.600 0.2 1 79 210 25 PHE N N 121.100 0.2 1 80 211 26 PHE H H 8.420 0.01 1 81 211 26 PHE CA C 59.300 0.2 1 82 211 26 PHE CB C 39.200 0.2 1 83 211 26 PHE N N 118.300 0.2 1 84 212 27 SER H H 8.080 0.01 1 85 212 27 SER CA C 59.900 0.2 1 86 212 27 SER CB C 63.600 0.2 1 87 212 27 SER N N 116.100 0.2 1 88 213 28 GLN H H 7.950 0.01 1 89 213 28 GLN CA C 56.800 0.2 1 90 213 28 GLN CB C 29.500 0.2 1 91 213 28 GLN N N 120.300 0.2 1 92 214 29 TYR H H 8.030 0.01 1 93 214 29 TYR CA C 58.200 0.2 1 94 214 29 TYR CB C 39.300 0.2 1 95 214 29 TYR N N 118.700 0.2 1 96 215 30 GLY H H 8.100 0.01 1 97 215 30 GLY CA C 45.600 0.2 1 98 215 30 GLY N N 109.400 0.2 1 99 216 31 ASP H H 8.290 0.01 1 100 216 31 ASP CA C 54.600 0.2 1 101 216 31 ASP N N 120.200 0.2 1 102 219 34 ASP CA C 54.300 0.2 1 103 219 34 ASP CB C 41.700 0.2 1 104 220 35 VAL H H 8.100 0.01 1 105 220 35 VAL CA C 62.300 0.2 1 106 220 35 VAL CB C 33.300 0.2 1 107 220 35 VAL N N 119.000 0.2 1 108 221 36 PHE H H 8.280 0.01 1 109 221 36 PHE CA C 57.900 0.2 1 110 221 36 PHE CB C 39.300 0.2 1 111 221 36 PHE N N 123.100 0.2 1 112 226 41 PHE H H 8.090 0.01 1 113 226 41 PHE CA C 55.500 0.2 1 114 226 41 PHE CB C 42.200 0.2 1 115 226 41 PHE N N 121.800 0.2 1 116 227 42 ARG H H 8.490 0.01 1 117 227 42 ARG CA C 55.700 0.2 1 118 227 42 ARG N N 119.000 0.2 1 119 229 44 PHE H H 8.070 0.01 1 120 229 44 PHE CA C 57.500 0.2 1 121 229 44 PHE CB C 39.900 0.2 1 122 229 44 PHE N N 119.100 0.2 1 123 230 45 ALA H H 8.120 0.01 1 124 230 45 ALA CA C 52.600 0.2 1 125 230 45 ALA CB C 19.500 0.2 1 126 230 45 ALA N N 125.000 0.2 1 127 231 46 PHE H H 8.140 0.01 1 128 231 46 PHE CA C 57.700 0.2 1 129 231 46 PHE CB C 39.900 0.2 1 130 231 46 PHE N N 119.000 0.2 1 131 232 47 VAL H H 8.150 0.01 1 132 232 47 VAL CA C 62.200 0.2 1 133 232 47 VAL CB C 33.200 0.2 1 134 232 47 VAL N N 122.500 0.2 1 135 233 48 THR H H 8.120 0.01 1 136 233 48 THR CA C 61.500 0.2 1 137 233 48 THR CB C 70.100 0.2 1 138 233 48 THR N N 117.600 0.2 1 139 234 49 PHE H H 8.320 0.01 1 140 234 49 PHE CA C 57.600 0.2 1 141 234 49 PHE CB C 40.000 0.2 1 142 234 49 PHE N N 122.400 0.2 1 143 235 50 ALA H H 8.310 0.01 1 144 235 50 ALA CA C 52.700 0.2 1 145 235 50 ALA CB C 19.700 0.2 1 146 235 50 ALA N N 125.100 0.2 1 147 236 51 ASP H H 8.230 0.01 1 148 236 51 ASP CA C 56.000 0.2 1 149 236 51 ASP CB C 41.300 0.2 1 150 236 51 ASP N N 119.600 0.2 1 151 237 52 ASP H H 8.730 0.01 1 152 237 52 ASP CA C 54.700 0.2 1 153 237 52 ASP CB C 41.300 0.2 1 154 237 52 ASP N N 120.600 0.2 1 155 239 54 ILE H H 8.050 0.01 1 156 239 54 ILE CA C 61.500 0.2 1 157 239 54 ILE CB C 38.800 0.2 1 158 239 54 ILE N N 121.200 0.2 1 159 240 55 ALA H H 8.320 0.01 1 160 240 55 ALA CA C 52.900 0.2 1 161 240 55 ALA CB C 19.300 0.2 1 162 240 55 ALA N N 127.500 0.2 1 163 241 56 GLN H H 8.290 0.01 1 164 241 56 GLN CA C 56.200 0.2 1 165 241 56 GLN CB C 29.900 0.2 1 166 241 56 GLN N N 119.400 0.2 1 167 242 57 SER H H 8.350 0.01 1 168 242 57 SER CA C 58.600 0.2 1 169 242 57 SER CB C 63.800 0.2 1 170 242 57 SER N N 116.800 0.2 1 171 243 58 LEU H H 8.370 0.01 1 172 243 58 LEU CA C 55.600 0.2 1 173 243 58 LEU CB C 42.500 0.2 1 174 243 58 LEU N N 124.000 0.2 1 175 244 59 CYS CA C 55.600 0.2 1 176 244 59 CYS CB C 41.500 0.2 1 177 245 60 GLY H H 8.480 0.01 1 178 245 60 GLY CA C 45.700 0.2 1 179 245 60 GLY N N 110.800 0.2 1 180 246 61 GLU H H 8.360 0.01 1 181 246 61 GLU CA C 56.900 0.2 1 182 246 61 GLU CB C 30.600 0.2 1 183 246 61 GLU N N 120.700 0.2 1 184 247 62 ASP H H 8.450 0.01 1 185 247 62 ASP CA C 54.700 0.2 1 186 247 62 ASP CB C 41.300 0.2 1 187 247 62 ASP N N 120.700 0.2 1 188 248 63 LEU H H 8.260 0.01 1 189 248 63 LEU CA C 54.800 0.2 1 190 248 63 LEU CB C 41.300 0.2 1 191 248 63 LEU N N 120.000 0.2 1 192 249 64 ILE H H 7.890 0.01 1 193 249 64 ILE CA C 62.100 0.2 1 194 249 64 ILE CB C 36.000 0.2 1 195 249 64 ILE N N 118.700 0.2 1 196 250 65 ILE CA C 61.200 0.2 1 197 250 65 ILE CB C 38.900 0.2 1 198 251 66 LYS H H 8.410 0.01 1 199 251 66 LYS CA C 56.700 0.2 1 200 251 66 LYS CB C 36.300 0.2 1 201 251 66 LYS N N 125.500 0.2 1 202 252 67 GLY H H 8.260 0.01 1 203 252 67 GLY CA C 45.500 0.2 1 204 252 67 GLY N N 109.400 0.2 1 205 253 68 ILE H H 8.000 0.01 1 206 253 68 ILE CA C 61.100 0.2 1 207 253 68 ILE CB C 39.300 0.2 1 208 253 68 ILE N N 119.600 0.2 1 209 254 69 SER H H 8.420 0.01 1 210 254 69 SER CA C 58.200 0.2 1 211 254 69 SER CB C 63.900 0.2 1 212 254 69 SER N N 119.900 0.2 1 213 255 70 VAL H H 8.170 0.01 1 214 255 70 VAL CA C 62.100 0.2 1 215 255 70 VAL CB C 33.300 0.2 1 216 255 70 VAL N N 121.800 0.2 1 217 256 71 HIS CA C 55.900 0.2 1 218 256 71 HIS CB C 30.800 0.2 1 219 257 72 ILE H H 8.210 0.01 1 220 257 72 ILE CA C 61.000 0.2 1 221 257 72 ILE CB C 39.000 0.2 1 222 257 72 ILE N N 123.900 0.2 1 223 258 73 SER H H 8.460 0.01 1 224 258 73 SER CA C 58.200 0.2 1 225 258 73 SER CB C 64.000 0.2 1 226 258 73 SER N N 120.000 0.2 1 227 259 74 ASN H H 8.530 0.01 1 228 259 74 ASN CA C 53.300 0.2 1 229 259 74 ASN CB C 39.100 0.2 1 230 259 74 ASN N N 121.400 0.2 1 231 260 75 ALA H H 8.250 0.01 1 232 260 75 ALA CA C 52.500 0.2 1 233 260 75 ALA CB C 19.600 0.2 1 234 260 75 ALA N N 124.500 0.2 1 235 261 76 GLU H H 8.060 0.01 1 236 261 76 GLU CA C 57.700 0.2 1 237 261 76 GLU N N 119.200 0.2 1 stop_ save_