data_4651 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Helix 7 Bovine Rhodopsin ; _BMRB_accession_number 4651 _BMRB_flat_file_name bmr4651.str _Entry_type original _Submission_date 2000-07-20 _Accession_date 2001-03-16 _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 Yeagle P. L. . 2 Danis C. . . 3 Choi G. . . 4 Alderfer J. . . 5 Albert A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 142 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2001-05-09 original author . stop_ _Original_release_date 2001-05-09 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Three Dimensional Structure of the Seventh Transmembrane Helical Domain of the G-Protein Receptor, Rhodopsin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10930473 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Yeagle P. L. . 2 Danis C. . . 3 Choi G. . . 4 Alderfer J. . . 5 Albert A. . . stop_ _Journal_abbreviation 'Mol. Vis.' _Journal_name_full 'Molecular Vision' _Journal_volume 6 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 125 _Page_last 131 _Year 2000 _Details . loop_ _Keyword helix stop_ save_ ################################## # Molecular system description # ################################## save_system_Rhodopsin _Saveframe_category molecular_system _Mol_system_name Rhodopsin _Abbreviation_common Rhodopsin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Rhodopsin $Rhodopsin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Rhodopsin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Rhodopsin _Abbreviation_common Rhodopsin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; PAFFAKTSAVYNPVIYIMMN KQFRN ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 ALA 3 PHE 4 PHE 5 ALA 6 LYS 7 THR 8 SER 9 ALA 10 VAL 11 TYR 12 ASN 13 PRO 14 VAL 15 ILE 16 TYR 17 ILE 18 MET 19 MET 20 ASN 21 LYS 22 GLN 23 PHE 24 ARG 25 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-24 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 1F88 "Crystal Structure Of Bovine Rhodopsin" 100.00 348 100.00 100.00 4.61e-07 PDB 1FDF "Helix 7 Bovine Rhodopsin" 100.00 25 100.00 100.00 7.52e-08 PDB 1GZM "Structure Of Bovine Rhodopsin In A Trigonal Crystal Form" 100.00 349 100.00 100.00 4.63e-07 PDB 1HZX "Crystal Structure Of Bovine Rhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 1JFP "Structure Of Bovine Rhodopsin (Dark Adapted)" 100.00 348 100.00 100.00 4.61e-07 PDB 1L9H "Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution" 100.00 349 100.00 100.00 4.63e-07 PDB 1LN6 "Structure Of Bovine Rhodopsin (Metarhodopsin Ii)" 100.00 348 100.00 100.00 4.61e-07 PDB 1U19 "Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution" 100.00 349 100.00 100.00 4.63e-07 PDB 2G87 "Crystallographic Model Of Bathorhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2HPY "Crystallographic Model Of Lumirhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2I35 "Crystal Structure Of Rhombohedral Crystal Form Of Ground-State Rhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2I36 "Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2I37 "Crystal Structure Of A Photoactivated Rhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2J4Y "Crystal Structure Of A Rhodopsin Stabilizing Mutant Expressed In Mammalian Cells" 100.00 349 100.00 100.00 4.41e-07 PDB 2PED "Crystallographic Model Of 9-Cis-Rhodopsin" 100.00 349 100.00 100.00 4.63e-07 PDB 2X72 "Crystal Structure Of The Constitutively Active E113q,N2c, D282c Rhodopsin Mutant With Bound Galphact Peptide" 100.00 349 100.00 100.00 4.45e-07 PDB 3C9L "Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form" 100.00 348 100.00 100.00 4.61e-07 PDB 3C9M "Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form" 100.00 348 100.00 100.00 4.39e-07 PDB 3CAP "Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State" 100.00 348 100.00 100.00 4.61e-07 PDB 3DQB "Crystal Structure Of The Active G-protein-coupled Receptor Opsin In Complex With A C-terminal Peptide Derived From The Galpha S" 100.00 348 100.00 100.00 4.61e-07 PDB 3OAX "Crystal Structure Of Bovine Rhodopsin With Beta-Ionone" 100.00 349 100.00 100.00 4.63e-07 PDB 3PQR "Crystal Structure Of Metarhodopsin Ii In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin" 100.00 348 100.00 100.00 4.61e-07 PDB 3PXO "Crystal Structure Of Metarhodopsin Ii" 100.00 348 100.00 100.00 4.61e-07 PDB 4A4M "Crystal Structure Of The Light-Activated Constitutively Active N2c,M257y,D282c Rhodopsin Mutant In Complex With A Peptide Resem" 100.00 349 100.00 100.00 4.41e-07 PDB 4BEY "Night Blindness Causing G90d Rhodopsin In Complex With Gact2 Peptide" 100.00 349 100.00 100.00 4.32e-07 PDB 4BEZ "Night Blindness Causing G90d Rhodopsin In The Active Conformation" 100.00 349 100.00 100.00 4.32e-07 PDB 4J4Q "Crystal Structure Of Active Conformation Of Gpcr Opsin Stabilized By Octylglucoside" 100.00 348 100.00 100.00 4.61e-07 PDB 4PXF "Crystal Structure Of The Active G-protein-coupled Receptor Opsin In Complex With The Finger-loop Peptide Derived From The Full-" 100.00 348 100.00 100.00 4.61e-07 PDB 4X1H "Opsin/g(alpha) Peptide Complex Stabilized By Nonyl-glucoside" 100.00 348 100.00 100.00 4.61e-07 DBJ BAB83621 "rhodopsin [synthetic construct]" 100.00 348 100.00 100.00 4.61e-07 GB AAA30674 "rhodopsin [Bos taurus]" 100.00 348 100.00 100.00 4.61e-07 GB AAA30675 "rhodopsin, partial [Bos taurus]" 100.00 343 100.00 100.00 4.80e-07 GB ELR51227 "Rhodopsin, partial [Bos mutus]" 100.00 351 100.00 100.00 4.53e-07 PRF 0811197A rhodopsin 100.00 347 100.00 100.00 4.51e-07 PRF 0901188A rhodopsin 100.00 348 100.00 100.00 4.61e-07 PRF 0901212A rhodopsin 100.00 348 100.00 100.00 4.61e-07 PRF 0906201A rhodopsin 100.00 299 100.00 100.00 4.51e-07 PRF 1001148A rhodopsin 100.00 348 100.00 100.00 4.61e-07 REF NP_001014890 "rhodopsin [Bos taurus]" 100.00 348 100.00 100.00 4.61e-07 REF XP_005902896 "PREDICTED: rhodopsin [Bos mutus]" 100.00 348 100.00 100.00 4.26e-07 REF XP_010860750 "PREDICTED: rhodopsin [Bison bison bison]" 100.00 348 100.00 100.00 4.75e-07 SP P02699 "RecName: Full=Rhodopsin" 100.00 348 100.00 100.00 4.61e-07 TPG DAA16827 "TPA: rhodopsin [Bos taurus]" 100.00 348 100.00 100.00 4.61e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Rhodopsin 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 $Rhodopsin . . . . . . 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 $Rhodopsin . mM . DMSO . % . stop_ save_ ############################ # Computer software used # ############################ save_DIANA _Saveframe_category software _Name DIANA _Version 1 loop_ _Task 'structure solution' stop_ _Details Wuthrich save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 303 . K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_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_citation_label _Correction_value_citation_label . H 1 . ppm . . . . . . $entry_citation $entry_citation 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name Rhodopsin _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 PRO HA H 4.13 . . 2 . 1 PRO HB2 H 2.19 . . 3 . 1 PRO HB3 H 2.19 . . 4 . 2 ALA H H 8.55 . . 5 . 2 ALA HA H 4.3 . . 6 . 2 ALA HB H 1.15 . . 7 . 3 PHE H H 7.96 . . 8 . 3 PHE HA H 4.46 . . 9 . 3 PHE HB2 H 2.72 . . 10 . 3 PHE HB3 H 2.96 . . 11 . 3 PHE HD1 H 7.17 . . 12 . 3 PHE HD2 H 7.17 . . 13 . 4 PHE H H 8.1 . . 14 . 4 PHE HA H 4.56 . . 15 . 4 PHE HB2 H 2.79 . . 16 . 4 PHE HB3 H 3.03 . . 17 . 4 PHE HD1 H 7.24 . . 18 . 4 PHE HD2 H 7.24 . . 19 . 5 ALA H H 8.14 . . 20 . 5 ALA HA H 4.33 . . 21 . 5 ALA HB H 1.25 . . 22 . 6 LYS H H 8.08 . . 23 . 6 LYS HA H 4.32 . . 24 . 6 LYS HB2 H 1.51 . . 25 . 6 LYS HB3 H 1.72 . . 26 . 6 LYS HG2 H 1.34 . . 27 . 6 LYS HG3 H 1.34 . . 28 . 6 LYS HD2 H 2.76 . . 29 . 6 LYS HD3 H 2.76 . . 30 . 7 THR H H 7.69 . . 31 . 7 THR HA H 4.34 . . 32 . 7 THR HG2 H 1.03 . . 33 . 8 SER H H 7.84 . . 34 . 8 SER HA H 4.33 . . 35 . 8 SER HB2 H 3.56 . . 36 . 8 SER HB3 H 3.64 . . 37 . 9 ALA H H 8.06 . . 38 . 9 ALA HA H 4.3 . . 39 . 9 ALA HB H 1.19 . . 40 . 10 VAL H H 7.64 . . 41 . 10 VAL HA H 4.09 . . 42 . 10 VAL HB H 1.9 . . 43 . 10 VAL HG1 H 0.75 . . 44 . 10 VAL HG2 H 0.75 . . 45 . 11 TYR H H 7.79 . . 46 . 11 TYR HA H 4.47 . . 47 . 11 TYR HB2 H 2.66 . . 48 . 11 TYR HB3 H 2.84 . . 49 . 11 TYR HD1 H 6.95 . . 50 . 11 TYR HD2 H 6.95 . . 51 . 11 TYR HE1 H 6.59 . . 52 . 11 TYR HE2 H 6.59 . . 53 . 12 ASN H H 8.24 . . 54 . 12 ASN HA H 4.77 . . 55 . 12 ASN HB2 H 2.37 . . 56 . 12 ASN HB3 H 2.61 . . 57 . 12 ASN HD21 H 7.47 . . 58 . 12 ASN HD22 H 6.94 . . 59 . 13 PRO HA H 4.33 . . 60 . 13 PRO HB2 H 1.84 . . 61 . 13 PRO HB3 H 1.98 . . 62 . 13 PRO HG2 H 3.51 . . 63 . 13 PRO HG3 H 3.51 . . 64 . 13 PRO HD2 H 3.58 . . 65 . 13 PRO HD3 H 3.58 . . 66 . 14 VAL H H 7.79 . . 67 . 14 VAL HA H 3.94 . . 68 . 14 VAL HB H 1.99 . . 69 . 14 VAL HG1 H 0.84 . . 70 . 14 VAL HG2 H 0.80 . . 71 . 15 ILE H H 7.5 . . 72 . 15 ILE HA H 4.05 . . 73 . 15 ILE HB H 1.68 . . 74 . 15 ILE HG12 H 1.30 . . 75 . 15 ILE HG13 H 1.04 . . 76 . 15 ILE HG2 H 0.72 . . 77 . 16 TYR H H 7.76 . . 78 . 16 TYR HA H 4.43 . . 79 . 16 TYR HB2 H 2.70 . . 80 . 16 TYR HB3 H 2.88 . . 81 . 16 TYR HD1 H 6.96 . . 82 . 16 TYR HD2 H 6.96 . . 83 . 16 TYR HE1 H 6.60 . . 84 . 16 TYR HE2 H 6.60 . . 85 . 17 ILE H H 7.77 . . 86 . 17 ILE HA H 4.1 . . 87 . 17 ILE HB H 1.75 . . 88 . 17 ILE HG12 H 0.82 . . 89 . 17 ILE HG13 H 1.11 . . 90 . 17 ILE HG2 H 1.46 . . 91 . 18 MET H H 7.95 . . 92 . 18 MET HA H 4.3 . . 93 . 18 MET HB2 H 1.81 . . 94 . 18 MET HB3 H 1.91 . . 95 . 18 MET HG2 H 2.43 . . 96 . 18 MET HG3 H 2.43 . . 97 . 19 MET H H 7.88 . . 98 . 19 MET HA H 4.31 . . 99 . 19 MET HB2 H 1.78 . . 100 . 19 MET HB3 H 1.89 . . 101 . 19 MET HG2 H 2.46 . . 102 . 19 MET HG3 H 2.46 . . 103 . 20 ASN H H 8.09 . . 104 . 20 ASN HA H 4.51 . . 105 . 20 ASN HB2 H 2.44 . . 106 . 20 ASN HB3 H 2.55 . . 107 . 20 ASN HD21 H 6.90 . . 108 . 20 ASN HD22 H 7.39 . . 109 . 21 LYS H H 7.88 . . 110 . 21 LYS HA H 4.17 . . 111 . 21 LYS HB2 H 1.50 . . 112 . 21 LYS HB3 H 1.68 . . 113 . 21 LYS HG2 H 1.28 . . 114 . 21 LYS HG3 H 1.28 . . 115 . 21 LYS HD2 H 2.73 . . 116 . 21 LYS HD3 H 2.73 . . 117 . 22 GLN H H 7.88 . . 118 . 22 GLN HA H 4.16 . . 119 . 22 GLN HB2 H 1.84 . . 120 . 22 GLN HB3 H 1.69 . . 121 . 22 GLN HG2 H 2.07 . . 122 . 22 GLN HG3 H 2.07 . . 123 . 22 GLN HE21 H 6.78 . . 124 . 22 GLN HE22 H 6.78 . . 125 . 23 PHE H H 7.88 . . 126 . 23 PHE HA H 4.51 . . 127 . 23 PHE HB2 H 2.80 . . 128 . 23 PHE HB3 H 3.03 . . 129 . 23 PHE HD1 H 7.22 . . 130 . 23 PHE HD2 H 7.22 . . 131 . 24 ARG H H 8.08 . . 132 . 24 ARG HA H 4.32 . . 133 . 24 ARG HB2 H 1.71 . . 134 . 24 ARG HB3 H 1.71 . . 135 . 24 ARG HG2 H 1.50 . . 136 . 24 ARG HG3 H 1.50 . . 137 . 24 ARG HD2 H 3.10 . . 138 . 24 ARG HD3 H 3.10 . . 139 . 25 ASN H H 8.13 . . 140 . 25 ASN HA H 4.53 . . 141 . 25 ASN HB2 H 2.48 . . 142 . 25 ASN HB3 H 2.55 . . stop_ save_