data_26812 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 13C Chemical Shifts rhodopsion ; _BMRB_accession_number 26812 _BMRB_flat_file_name bmr26812.str _Entry_type original _Submission_date 2016-06-12 _Accession_date 2016-06-12 _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 Kimata Naoki . . 2 Pope Andreyah . . 3 Eilers Markus . . 4 Opefi Chikwado A. . 5 Ziliox Martine . . 6 Hirschfeld Amiram . . 7 Zaitseva Ekaterina . . 8 Vogel Reiner . . 9 Sheves Mordechai . . 10 Reeves Philip J. . 11 Smith Steven O. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 36 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-10-26 update BMRB 'update entry citation' 2016-06-16 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 26811 rhodopsin 26813 'Complex II of Retinal and Metarhodopsin II' stop_ _Original_release_date 2016-06-16 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27585742 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kimata Naoki . . 2 Pope Andreyah . . 3 Eilers Markus . . 4 Opefi Chikwado A. . 5 Ziliox Martine . . 6 Hirschfeld Amiram . . 7 Zaitseva Ekaterina . . 8 Vogel Reiner . . 9 Sheves Mordechai . . 10 Vogel Reiner J. . 11 Smith Steven O. . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_volume 7 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12683 _Page_last 12683 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Rhodopsin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Opsin $Opsin Retinal $entity_RET 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_Opsin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Opsin _Molecular_mass . _Mol_thiol_state 'free and disulfide bound' _Details 'Cys110-Cys187 disulfide bond' ############################## # Polymer residue sequence # ############################## _Residue_count 348 _Mol_residue_sequence ; MNGTEGPNFYVPFSNKTGVV RSPFEAPQYYLAEPWQFSML AAYMFLLIMLGFPINFLTLY VTVQHKKLRTPLNYILLNLA VADLFMVFGGFTTTLYTSLH GYFVFGPTGCNLEGFFATLG GEIALWSLVVLAIERYVVVC KPMSNFRFGENHAIMGVAFT WVMALACAAPPLVGWSRYIP EGMQCSCGIDYYTPHEETNN ESFVIYMFVVHFIIPLIVIF FCYGQLVFTVKEAAAQQQES ATTQKAEKEVTRMVIIMVIA FLICWLPYAGVAFYIFTHQG SDFGPIFMTIPAFFAKTSSV YNPVIYIMMNKQFRNCMVTT LCCGKNPLGDDEASTTVSKT ETSQVAPA ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ASN 3 GLY 4 THR 5 GLU 6 GLY 7 PRO 8 ASN 9 PHE 10 TYR 11 VAL 12 PRO 13 PHE 14 SER 15 ASN 16 LYS 17 THR 18 GLY 19 VAL 20 VAL 21 ARG 22 SER 23 PRO 24 PHE 25 GLU 26 ALA 27 PRO 28 GLN 29 TYR 30 TYR 31 LEU 32 ALA 33 GLU 34 PRO 35 TRP 36 GLN 37 PHE 38 SER 39 MET 40 LEU 41 ALA 42 ALA 43 TYR 44 MET 45 PHE 46 LEU 47 LEU 48 ILE 49 MET 50 LEU 51 GLY 52 PHE 53 PRO 54 ILE 55 ASN 56 PHE 57 LEU 58 THR 59 LEU 60 TYR 61 VAL 62 THR 63 VAL 64 GLN 65 HIS 66 LYS 67 LYS 68 LEU 69 ARG 70 THR 71 PRO 72 LEU 73 ASN 74 TYR 75 ILE 76 LEU 77 LEU 78 ASN 79 LEU 80 ALA 81 VAL 82 ALA 83 ASP 84 LEU 85 PHE 86 MET 87 VAL 88 PHE 89 GLY 90 GLY 91 PHE 92 THR 93 THR 94 THR 95 LEU 96 TYR 97 THR 98 SER 99 LEU 100 HIS 101 GLY 102 TYR 103 PHE 104 VAL 105 PHE 106 GLY 107 PRO 108 THR 109 GLY 110 CYS 111 ASN 112 LEU 113 GLU 114 GLY 115 PHE 116 PHE 117 ALA 118 THR 119 LEU 120 GLY 121 GLY 122 GLU 123 ILE 124 ALA 125 LEU 126 TRP 127 SER 128 LEU 129 VAL 130 VAL 131 LEU 132 ALA 133 ILE 134 GLU 135 ARG 136 TYR 137 VAL 138 VAL 139 VAL 140 CYS 141 LYS 142 PRO 143 MET 144 SER 145 ASN 146 PHE 147 ARG 148 PHE 149 GLY 150 GLU 151 ASN 152 HIS 153 ALA 154 ILE 155 MET 156 GLY 157 VAL 158 ALA 159 PHE 160 THR 161 TRP 162 VAL 163 MET 164 ALA 165 LEU 166 ALA 167 CYS 168 ALA 169 ALA 170 PRO 171 PRO 172 LEU 173 VAL 174 GLY 175 TRP 176 SER 177 ARG 178 TYR 179 ILE 180 PRO 181 GLU 182 GLY 183 MET 184 GLN 185 CYS 186 SER 187 CYS 188 GLY 189 ILE 190 ASP 191 TYR 192 TYR 193 THR 194 PRO 195 HIS 196 GLU 197 GLU 198 THR 199 ASN 200 ASN 201 GLU 202 SER 203 PHE 204 VAL 205 ILE 206 TYR 207 MET 208 PHE 209 VAL 210 VAL 211 HIS 212 PHE 213 ILE 214 ILE 215 PRO 216 LEU 217 ILE 218 VAL 219 ILE 220 PHE 221 PHE 222 CYS 223 TYR 224 GLY 225 GLN 226 LEU 227 VAL 228 PHE 229 THR 230 VAL 231 LYS 232 GLU 233 ALA 234 ALA 235 ALA 236 GLN 237 GLN 238 GLN 239 GLU 240 SER 241 ALA 242 THR 243 THR 244 GLN 245 LYS 246 ALA 247 GLU 248 LYS 249 GLU 250 VAL 251 THR 252 ARG 253 MET 254 VAL 255 ILE 256 ILE 257 MET 258 VAL 259 ILE 260 ALA 261 PHE 262 LEU 263 ILE 264 CYS 265 TRP 266 LEU 267 PRO 268 TYR 269 ALA 270 GLY 271 VAL 272 ALA 273 PHE 274 TYR 275 ILE 276 PHE 277 THR 278 HIS 279 GLN 280 GLY 281 SER 282 ASP 283 PHE 284 GLY 285 PRO 286 ILE 287 PHE 288 MET 289 THR 290 ILE 291 PRO 292 ALA 293 PHE 294 PHE 295 ALA 296 LYS 297 THR 298 SER 299 SER 300 VAL 301 TYR 302 ASN 303 PRO 304 VAL 305 ILE 306 TYR 307 ILE 308 MET 309 MET 310 ASN 311 LYS 312 GLN 313 PHE 314 ARG 315 ASN 316 CYS 317 MET 318 VAL 319 THR 320 THR 321 LEU 322 CYS 323 CYS 324 GLY 325 LYS 326 ASN 327 PRO 328 LEU 329 GLY 330 ASP 331 ASP 332 GLU 333 ALA 334 SER 335 THR 336 THR 337 VAL 338 SER 339 LYS 340 THR 341 GLU 342 THR 343 SER 344 GLN 345 VAL 346 ALA 347 PRO 348 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_RET _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_RET (RETINAL)" _BMRB_code RET _PDB_code RET _Molecular_mass 284.436 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? C14 C14 C . 0 . ? C15 C15 C . 0 . ? O1 O1 O . 0 . ? C16 C16 C . 0 . ? C17 C17 C . 0 . ? C18 C18 C . 0 . ? C19 C19 C . 0 . ? C20 C20 C . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H14 H14 H . 0 . ? H15 H15 H . 0 . ? H161 H161 H . 0 . ? H162 H162 H . 0 . ? H163 H163 H . 0 . ? H171 H171 H . 0 . ? H172 H172 H . 0 . ? H173 H173 H . 0 . ? H181 H181 H . 0 . ? H182 H182 H . 0 . ? H183 H183 H . 0 . ? H191 H191 H . 0 . ? H192 H192 H . 0 . ? H193 H193 H . 0 . ? H201 H201 H . 0 . ? H202 H202 H . 0 . ? H203 H203 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING C1 C2 ? ? SING C1 C6 ? ? SING C1 C16 ? ? SING C1 C17 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 C4 ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C4 C5 ? ? SING C4 H41 ? ? SING C4 H42 ? ? DOUB C5 C6 ? ? SING C5 C18 ? ? SING C6 C7 ? ? DOUB C7 C8 ? ? SING C7 H7 ? ? SING C8 C9 ? ? SING C8 H8 ? ? DOUB C9 C10 ? ? SING C9 C19 ? ? SING C10 C11 ? ? SING C10 H10 ? ? DOUB C11 C12 ? ? SING C11 H11 ? ? SING C12 C13 ? ? SING C12 H12 ? ? DOUB C13 C14 ? ? SING C13 C20 ? ? SING C14 C15 ? ? SING C14 H14 ? ? DOUB C15 O1 ? ? SING C15 H15 ? ? SING C16 H161 ? ? SING C16 H162 ? ? SING C16 H163 ? ? SING C17 H171 ? ? SING C17 H172 ? ? SING C17 H173 ? ? SING C18 H181 ? ? SING C18 H182 ? ? SING C18 H183 ? ? SING C19 H191 ? ? SING C19 H192 ? ? SING C19 H193 ? ? SING C20 H201 ? ? SING C20 H202 ? ? SING C20 H203 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Opsin cow 9913 Eukaryota Metazoa Bos taurus 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 _Details $Opsin 'recombinant technology' . . . . pACHrhoC 'Human embryonic kidney cells' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Opsin 5 mg 'Specific 13C' $entity_RET 50 ug 'Specific 13C' 'sodium phosphate' 2 mM 'natural abundance' DDM 0.02 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing 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_2D_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DARR' _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' 2 . mM pH 6 . pH pressure 1 . atm temperature 190 . 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 glycine C 13 carbonyl ppm 176.46 external direct . . . 1 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DARR' 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 Opsin _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 44 44 MET CE C 10.5 0.2 1 2 86 86 MET CE C 13.6 0.2 1 3 110 110 CYS C C 172.0 0.2 1 4 114 114 GLY CA C 45.5 0.2 1 5 121 121 GLY CA C 46.0 0.2 1 6 178 178 TYR CZ C 157.6 0.2 1 7 186 186 SER CB C 63.3 0.2 1 8 187 187 CYS C C 170.8 0.2 1 9 188 188 GLY CA C 42.0 0.2 1 10 191 191 TYR CZ C 159.3 0.2 1 11 206 206 TYR CZ C 154.8 0.2 1 12 207 207 MET C C 175.2 0.2 1 13 207 207 MET CE C 13.5 0.2 1 14 211 211 HIS C C 172.4 0.2 1 15 257 257 MET CE C 13.8 0.2 1 16 261 261 PHE CG C 137.0 0.2 1 17 261 261 PHE CD1 C 129.0 0.2 3 18 261 261 PHE CD2 C 129.0 0.2 3 19 261 261 PHE CE1 C 129.0 0.2 3 20 261 261 PHE CE2 C 129.0 0.2 3 21 261 261 PHE CZ C 129.0 0.2 1 22 268 268 TYR CZ C 156.1 0.2 1 23 288 288 MET CE C 17.2 0.2 1 24 298 298 SER CB C 61.2 0.2 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DARR' 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 Retinal _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 1 RET C5 C 131.0 0.1 1 2 8 1 RET C8 C 139.3 0.1 1 3 10 1 RET C10 C 128.0 0.1 1 4 11 1 RET C11 C 141.6 0.1 1 5 12 1 RET C12 C 132.2 0.1 1 6 14 1 RET C14 C 122.1 0.1 1 7 15 1 RET C15 C 165.7 0.1 1 8 16 1 RET C16 C 30.6 0.1 1 9 17 1 RET C17 C 26.1 0.1 1 10 18 1 RET C18 C 21.6 0.1 1 11 19 1 RET C19 C 14.7 0.1 1 12 20 1 RET C20 C 16.4 0.1 1 stop_ save_