data_26605 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Methyl resonances of Ubiquitin-like domain (1-76) of parkin in complex with R0RBR domain (141-465) of parkin. ; _BMRB_accession_number 26605 _BMRB_flat_file_name bmr26605.str _Entry_type original _Submission_date 2015-07-10 _Accession_date 2015-07-10 _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 Aguirre Jacob D. . 2 Shaw Gary S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 30 "13C chemical shifts" 30 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-12-05 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 5500 'parkin ubiquitin-like domain' stop_ _Original_release_date 2015-07-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26254304 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kumar Atul . . 2 Aguirre Jacob D. . 3 Condos Tara EC . 4 Martinez-Torres 'R. Julio' . . 5 Chaugule Viduth K. . 6 Toth Rachel . . 7 Sundaramoorthy Ramasubramanian . . 8 Mercier Pascal . . 9 Knebel Axel . . 10 Spratt Donald E. . 11 Barber Kathryn R. . 12 Shaw Gary S. . 13 Walden Helen . . stop_ _Journal_abbreviation 'EMBO J.' _Journal_volume 34 _Journal_issue 20 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2506 _Page_last 2521 _Year 2015 _Details . loop_ _Keyword Ubl Ubld parkin phosphoubiquitin 'ubiquitin-like domain' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'UblD in complex with parkin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'UblD, chain 1' $parkin_ubiquitin-like_domain_(1-76) 'UblD, chain 2' $parkin_ubiquitin-like_domain_(1-76) 'parkin, 141-465' $parkin_(141-465) 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_parkin_ubiquitin-like_domain_(1-76) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common parkin_ubiquitin-like_domain_(1-76) _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 76 _Mol_residue_sequence ; MIVFVRFNSSHGFPVEVDSD TSIFQLKEVVAKRQGVPADQ LRVIFAGKELRNDWTVQNCD LDQQSIVHIVQRPWRK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ILE 3 VAL 4 PHE 5 VAL 6 ARG 7 PHE 8 ASN 9 SER 10 SER 11 HIS 12 GLY 13 PHE 14 PRO 15 VAL 16 GLU 17 VAL 18 ASP 19 SER 20 ASP 21 THR 22 SER 23 ILE 24 PHE 25 GLN 26 LEU 27 LYS 28 GLU 29 VAL 30 VAL 31 ALA 32 LYS 33 ARG 34 GLN 35 GLY 36 VAL 37 PRO 38 ALA 39 ASP 40 GLN 41 LEU 42 ARG 43 VAL 44 ILE 45 PHE 46 ALA 47 GLY 48 LYS 49 GLU 50 LEU 51 ARG 52 ASN 53 ASP 54 TRP 55 THR 56 VAL 57 GLN 58 ASN 59 CYS 60 ASP 61 LEU 62 ASP 63 GLN 64 GLN 65 SER 66 ILE 67 VAL 68 HIS 69 ILE 70 VAL 71 GLN 72 ARG 73 PRO 74 TRP 75 ARG 76 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_parkin_(141-465) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common parkin_(141-465) _Molecular_mass . _Mol_thiol_state 'free and other bound' _Details '8 Zinc atoms coordinated by cysteines' _Residue_count 325 _Mol_residue_sequence ; SIYNSFYVYCKGPCQRVQPG KLRVQCSTCRQATLTLTQGP SCWDDVLIPNRMSGECQSPH CPGTSAEFFFKCGAHPTSDK ETSVALHLIATNSRNITCIT CTDVRSPVLVFQCNSRHVIC LDCFHLYCVTRLNDRQFVHD PQLGYSLPCVAGCPNSLIKE LHHFRILGEEQYNRYQQYGA EECVLQMGGVLCPRPGCGAG LLPEPDQRKVTCEGGNGLGC GFAFCRECKEAYHEGECSAV FEASGTTTQAYRVDERAAEQ ARWEAASKETIKKTTKPCPR CHVPVEKNGGCMHMKCPQPQ CRLEWCWNCGCEWNRVCMGD HWFDV ; loop_ _Residue_seq_code _Residue_label 1 SER 2 ILE 3 TYR 4 ASN 5 SER 6 PHE 7 TYR 8 VAL 9 TYR 10 CYS 11 LYS 12 GLY 13 PRO 14 CYS 15 GLN 16 ARG 17 VAL 18 GLN 19 PRO 20 GLY 21 LYS 22 LEU 23 ARG 24 VAL 25 GLN 26 CYS 27 SER 28 THR 29 CYS 30 ARG 31 GLN 32 ALA 33 THR 34 LEU 35 THR 36 LEU 37 THR 38 GLN 39 GLY 40 PRO 41 SER 42 CYS 43 TRP 44 ASP 45 ASP 46 VAL 47 LEU 48 ILE 49 PRO 50 ASN 51 ARG 52 MET 53 SER 54 GLY 55 GLU 56 CYS 57 GLN 58 SER 59 PRO 60 HIS 61 CYS 62 PRO 63 GLY 64 THR 65 SER 66 ALA 67 GLU 68 PHE 69 PHE 70 PHE 71 LYS 72 CYS 73 GLY 74 ALA 75 HIS 76 PRO 77 THR 78 SER 79 ASP 80 LYS 81 GLU 82 THR 83 SER 84 VAL 85 ALA 86 LEU 87 HIS 88 LEU 89 ILE 90 ALA 91 THR 92 ASN 93 SER 94 ARG 95 ASN 96 ILE 97 THR 98 CYS 99 ILE 100 THR 101 CYS 102 THR 103 ASP 104 VAL 105 ARG 106 SER 107 PRO 108 VAL 109 LEU 110 VAL 111 PHE 112 GLN 113 CYS 114 ASN 115 SER 116 ARG 117 HIS 118 VAL 119 ILE 120 CYS 121 LEU 122 ASP 123 CYS 124 PHE 125 HIS 126 LEU 127 TYR 128 CYS 129 VAL 130 THR 131 ARG 132 LEU 133 ASN 134 ASP 135 ARG 136 GLN 137 PHE 138 VAL 139 HIS 140 ASP 141 PRO 142 GLN 143 LEU 144 GLY 145 TYR 146 SER 147 LEU 148 PRO 149 CYS 150 VAL 151 ALA 152 GLY 153 CYS 154 PRO 155 ASN 156 SER 157 LEU 158 ILE 159 LYS 160 GLU 161 LEU 162 HIS 163 HIS 164 PHE 165 ARG 166 ILE 167 LEU 168 GLY 169 GLU 170 GLU 171 GLN 172 TYR 173 ASN 174 ARG 175 TYR 176 GLN 177 GLN 178 TYR 179 GLY 180 ALA 181 GLU 182 GLU 183 CYS 184 VAL 185 LEU 186 GLN 187 MET 188 GLY 189 GLY 190 VAL 191 LEU 192 CYS 193 PRO 194 ARG 195 PRO 196 GLY 197 CYS 198 GLY 199 ALA 200 GLY 201 LEU 202 LEU 203 PRO 204 GLU 205 PRO 206 ASP 207 GLN 208 ARG 209 LYS 210 VAL 211 THR 212 CYS 213 GLU 214 GLY 215 GLY 216 ASN 217 GLY 218 LEU 219 GLY 220 CYS 221 GLY 222 PHE 223 ALA 224 PHE 225 CYS 226 ARG 227 GLU 228 CYS 229 LYS 230 GLU 231 ALA 232 TYR 233 HIS 234 GLU 235 GLY 236 GLU 237 CYS 238 SER 239 ALA 240 VAL 241 PHE 242 GLU 243 ALA 244 SER 245 GLY 246 THR 247 THR 248 THR 249 GLN 250 ALA 251 TYR 252 ARG 253 VAL 254 ASP 255 GLU 256 ARG 257 ALA 258 ALA 259 GLU 260 GLN 261 ALA 262 ARG 263 TRP 264 GLU 265 ALA 266 ALA 267 SER 268 LYS 269 GLU 270 THR 271 ILE 272 LYS 273 LYS 274 THR 275 THR 276 LYS 277 PRO 278 CYS 279 PRO 280 ARG 281 CYS 282 HIS 283 VAL 284 PRO 285 VAL 286 GLU 287 LYS 288 ASN 289 GLY 290 GLY 291 CYS 292 MET 293 HIS 294 MET 295 LYS 296 CYS 297 PRO 298 GLN 299 PRO 300 GLN 301 CYS 302 ARG 303 LEU 304 GLU 305 TRP 306 CYS 307 TRP 308 ASN 309 CYS 310 GLY 311 CYS 312 GLU 313 TRP 314 ASN 315 ARG 316 VAL 317 CYS 318 MET 319 GLY 320 ASP 321 HIS 322 TRP 323 PHE 324 ASP 325 VAL 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 $parkin_ubiquitin-like_domain_(1-76) human 9606 Eukaryota Metazoa Homo sapiens $parkin_(141-465) 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 $parkin_ubiquitin-like_domain_(1-76) 'recombinant technology' . Escherichia coli . pet-SUMO $parkin_(141-465) 'recombinant technology' . Escherichia coli . pet-SUMO stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $parkin_ubiquitin-like_domain_(1-76) 200 uM '[U-99% 13C; U-99% 15N]' $parkin_(141-465) 300 uM '[U-99% 2H]' HEPES 25 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' TCEP 500 uM 'natural abundance' imidazole 500 uM 'natural abundance' DSS 100 uM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRView _Saveframe_category software _Name NMRView _Version 8.2.36 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 3.2 loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2010.160.15.01 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-13C_HMQC_aliphatic_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC aliphatic' _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 'ionic strength' 100 . mM pH 7.0 . pH pressure 1 . atm temperature 298.15 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Chemical shifts assigned by comparison with free UblD chemical shifts (ID 5500)' 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 carbon' ppm 0.0 external indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 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_ _Experiment_label '2D 1H-13C HMQC aliphatic' 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 'UblD, chain 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 1 1 MET HE H 1.6906 0.00325 1 2 1 1 MET CE C 17.1021 0.000176 1 3 2 2 ILE HG2 H 0.5351 0.00325 1 4 2 2 ILE HD1 H 0.6013 0.00325 1 5 2 2 ILE CG2 C 17.0009 0.000176 1 6 2 2 ILE CD1 C 12.1322 0.000176 1 7 3 3 VAL HG1 H 0.6289 0.00325 2 8 3 3 VAL HG2 H 0.6052 0.00325 2 9 3 3 VAL CG1 C 20.5364 0.000176 2 10 3 3 VAL CG2 C 21.7757 0.000176 2 11 17 17 VAL HG1 H 0.4910 0.00325 2 12 17 17 VAL CG1 C 19.2640 0.000176 2 13 21 21 THR HG2 H 1.3932 0.00325 1 14 21 21 THR CG2 C 21.7982 0.000176 1 15 23 23 ILE HG2 H 0.7554 0.00325 1 16 23 23 ILE HD1 H 0.6038 0.00325 1 17 23 23 ILE CG2 C 17.3599 0.000176 1 18 23 23 ILE CD1 C 7.8508 0.000176 1 19 26 26 LEU HD1 H 0.6425 0.00325 2 20 26 26 LEU HD2 H 0.6507 0.00325 2 21 26 26 LEU CD1 C 23.9507 0.000176 2 22 26 26 LEU CD2 C 25.2013 0.000176 2 23 29 29 VAL HG1 H 1.0266 0.00325 2 24 29 29 VAL HG2 H 1.0480 0.00325 2 25 29 29 VAL CG1 C 20.7054 0.000176 2 26 29 29 VAL CG2 C 22.1342 0.000176 2 27 30 30 VAL HG1 H 1.0372 0.00325 2 28 30 30 VAL CG1 C 23.2030 0.000176 2 29 31 31 ALA HB H 1.5572 0.00325 1 30 31 31 ALA CB C 19.1619 0.000176 1 31 38 38 ALA HB H 1.1698 0.00325 1 32 38 38 ALA CB C 18.4552 0.000176 1 33 44 44 ILE HG2 H 0.1490 0.00325 1 34 44 44 ILE HD1 H 0.6370 0.00325 1 35 44 44 ILE CG2 C 18.0232 0.000176 1 36 44 44 ILE CD1 C 11.4506 0.000176 1 37 46 46 ALA HB H 0.7306 0.00325 1 38 46 46 ALA CB C 16.5852 0.000176 1 39 50 50 LEU HD1 H 1.0725 0.00325 2 40 50 50 LEU HD2 H 1.2666 0.00325 2 41 50 50 LEU CD1 C 25.3379 0.000176 2 42 50 50 LEU CD2 C 21.8451 0.000176 2 43 55 55 THR HG2 H 1.1796 0.00325 1 44 55 55 THR CG2 C 22.0351 0.000176 1 45 61 61 LEU HD1 H -0.2358 0.00325 2 46 61 61 LEU HD2 H 0.4231 0.00325 2 47 61 61 LEU CD1 C 22.7327 0.000176 2 48 61 61 LEU CD2 C 25.2895 0.000176 2 49 66 66 ILE HG2 H 0.7220 0.00325 1 50 66 66 ILE HD1 H 0.9240 0.00325 1 51 66 66 ILE CG2 C 18.1733 0.000176 1 52 66 66 ILE CD1 C 13.8642 0.000176 1 53 69 69 ILE HG2 H 0.9736 0.00325 1 54 69 69 ILE HD1 H 0.6802 0.00325 1 55 69 69 ILE CG2 C 19.3616 0.000176 1 56 69 69 ILE CD1 C 13.2269 0.000176 1 57 70 70 VAL HG1 H 0.3811 0.00325 2 58 70 70 VAL HG2 H 0.4254 0.00325 2 59 70 70 VAL CG1 C 20.6820 0.000176 2 60 70 70 VAL CG2 C 22.5341 0.000176 2 stop_ save_