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2ped

Crystallographic model of 9-cis-rhodopsin

Method: X-RAY DIFFRACTION Dmax: 96.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rhodopsin

OrganismNot specified

UniProt P02699

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–348 Chain B； UniProt 1–348 Non-standard monomer：Yes (specific site not provided by mmCIF) alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M AMMONIUM SULFATE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K Resolution 2.95 Å R-free 0.289
2 Other combination Homooligomer Protein × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–348 Chain B； UniProt 1–348 Non-standard monomer：Yes (specific site not provided by mmCIF) alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M AMMONIUM SULFATE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K Resolution 2.95 Å R-free 0.289

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2PED Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EDS SOLUTION STRUCTURE OF INTRADISKAL LOOP 1 OF BOVINE RHODOPSIN (RHODOPSIN RESIDUES 92-123) Deposited 2000-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 93–123（31 aa） Fragment：FIRST INTRADISKAL LOOP (RESIDUES 93-123)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 303 K；Pressure 1
NMR sample composition 2 mM peptide | DMSO
Resolution not provided
1EDV SOLUTION STRUCTURE OF 2ND INTRADISKAL LOOP OF BOVINE RHODOPSIN (RESIDUES 172-205) Deposited 2000-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 172–205（34 aa） Fragment：SECOND INTRADISKAL LOOP (RESIDUES 172-205)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 303 K；Pressure 1
NMR sample composition 2 mM peptide | DMSO
Resolution not provided
1EDW SOLUTION STRUCTURE OF THIRD INTRADISKAL LOOP OF BOVINE RHODOPSIN (RESIDUES 268-293) Deposited 2000-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 268–293（26 aa） Fragment：THIRD INTRADISKAL LOOP (RESIDUES 268-293)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 303 K；Pressure 1
NMR sample composition 2 mM peptide | DMSO
Resolution not provided
1EDX SOLUTION STRUCTURE OF AMINO TERMINUS OF BOVINE RHODOPSIN (RESIDUES 1-40) Deposited 2000-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–40（40 aa） Fragment：AMINO TERMINAL (RESIDUES 1-40)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 303 K；Pressure 1
NMR sample composition 2 mM peptide | DMSO
Resolution not provided
1F88 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2000-06-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded HG MERCURY (II) ION × 6 ZN ZINC ION × 4 RET RETINAL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；MES, 2-mercaptoethanol, zinc acetate, heptanetriol, nonyl-glucoside, ammonium sulfate are in the hanging drops. mercury acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K
Resolution 2.80 Å R-free 0.238
1F88 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2000-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Not recorded HG MERCURY (II) ION × 3 ZN ZINC ION × 2 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；MES, 2-mercaptoethanol, zinc acetate, heptanetriol, nonyl-glucoside, ammonium sulfate are in the hanging drops. mercury acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K
Resolution 2.80 Å R-free 0.238
1F88 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2000-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Not recorded HG MERCURY (II) ION × 3 ZN ZINC ION × 2 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；MES, 2-mercaptoethanol, zinc acetate, heptanetriol, nonyl-glucoside, ammonium sulfate are in the hanging drops. mercury acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K
Resolution 2.80 Å R-free 0.238
1FDF HELIX 7 BOVINE RHODOPSIN Deposited 2000-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–315（25 aa） Fragment：HELIX 7, RESIDUES 291-315
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition peptide | DMSO
Resolution not provided
1GZM Structure of Bovine Rhodopsin in a Trigonal Crystal Form Deposited 2002-05-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 PLM PALMITIC ACID × 4 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 3 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 12 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；VAPOUR DIFFUSION IN SITTING DROPS OF 15 MG/ML PROTEIN AND 0.2% C8E4, 0.05%LDAO AGAINST 0.8M LI2SO4, 1.6% PEG8000 AND 20% GLYCEROL, pH 8.5
Resolution 2.65 Å R-free 0.235
1HZX CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2001-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 5 HG MERCURY (II) ION × 3 ZN ZINC ION × 4 PLM PALMITIC ACID × 2 RET RETINAL × 1 HTO HEPTANE-1,2,3-TRIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；MES, 2-MERCAPTOETHANOL, ZINC ACETATE, HEPTANETRIOL, NONYL-GLUCOSIDE, AMMONIUM SULFATE ARE IN THE HANGING DROPS. MERCURY ACETATE, pH 6.00
Resolution 2.80 Å R-free 0.212
1HZX CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2001-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 2 HG MERCURY (II) ION × 3 ZN ZINC ION × 3 PLM PALMITIC ACID × 1 RET RETINAL × 1 HTO HEPTANE-1,2,3-TRIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；MES, 2-MERCAPTOETHANOL, ZINC ACETATE, HEPTANETRIOL, NONYL-GLUCOSIDE, AMMONIUM SULFATE ARE IN THE HANGING DROPS. MERCURY ACETATE, pH 6.00
Resolution 2.80 Å R-free 0.212
1HZX CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2001-01-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 7 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 PLM PALMITIC ACID × 3 RET RETINAL × 2 HTO HEPTANE-1,2,3-TRIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；MES, 2-MERCAPTOETHANOL, ZINC ACETATE, HEPTANETRIOL, NONYL-GLUCOSIDE, AMMONIUM SULFATE ARE IN THE HANGING DROPS. MERCURY ACETATE, pH 6.00
Resolution 2.80 Å R-free 0.212
1HZX CRYSTAL STRUCTURE OF BOVINE RHODOPSIN Deposited 2001-01-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 7 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 PLM PALMITIC ACID × 3 RET RETINAL × 2 HTO HEPTANE-1,2,3-TRIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；MES, 2-MERCAPTOETHANOL, ZINC ACETATE, HEPTANETRIOL, NONYL-GLUCOSIDE, AMMONIUM SULFATE ARE IN THE HANGING DROPS. MERCURY ACETATE, pH 6.00
Resolution 2.80 Å R-free 0.212
1JFP Structure of bovine rhodopsin (dark adapted) Deposited 2001-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Not recorded RET RETINAL × 1 SOLUTION NMR
NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition fragments of rhodopsin | aqueous or DMSO
Resolution not provided
1L9H Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION Deposited 2002-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 5 HG MERCURY (II) ION × 3 ZN ZINC ION × 4 HTO HEPTANE-1,2,3-TRIOL × 4 PLM PALMITIC ACID × 3 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.60 Å R-free 0.225
1L9H Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION Deposited 2002-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 2 HG MERCURY (II) ION × 3 ZN ZINC ION × 3 PLM PALMITIC ACID × 2 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.60 Å R-free 0.225
1L9H Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION Deposited 2002-03-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 7 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 HTO HEPTANE-1,2,3-TRIOL × 4 PLM PALMITIC ACID × 5 RET RETINAL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.60 Å R-free 0.225
1L9H Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION Deposited 2002-03-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BNG nonyl beta-D-glucopyranoside × 7 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 HTO HEPTANE-1,2,3-TRIOL × 4 PLM PALMITIC ACID × 5 RET RETINAL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.60 Å R-free 0.225
1LN6 STRUCTURE OF BOVINE RHODOPSIN (Metarhodopsin II) Deposited 2002-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Not recorded RET RETINAL × 1 SOLUTION NMR
NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition FRAGMENTS OF RHODOPSIN | D2O, DMSO, DPC MICELLES
Resolution not provided
1NZS NMR structures of phosphorylated carboxy terminus of bovine rhodopsin in arrestin-bound state Deposited 2003-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 330–348（19 aa） Fragment：C-terminal domain, residues 330-348
Mutation：all serines and threonines phosphorylated Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；277 K；Ionic strength (raw mmCIF value) 0.1M phosphate；Pressure ambient
NMR sample composition 0.16 mM of purified arrestin, 1.77 mM of 7PP, 7-phospho-Rh(330-348) or unphosphorylated Rh(330-348) in sodium phosphate buffer, 0.1 M, pH 6.5 and 10% D2O in a total volume of 0.6 ml | 90% H2O/10% D2O
Resolution not provided
1U19 Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution Deposited 2004-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 3 ZN ZINC ION × 4 RET RETINAL × 1 PLM PALMITIC ACID × 3 HTG heptyl 1-thio-beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.20 Å R-free 0.222
1U19 Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution Deposited 2004-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 3 ZN ZINC ION × 3 RET RETINAL × 1 PLM PALMITIC ACID × 3 HTG heptyl 1-thio-beta-D-glucopyranoside × 3 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.20 Å R-free 0.222
1VQX ARRESTIN-BOUND NMR STRUCTURES OF THE PHOSPHORYLATED CARBOXY-TERMINAL DOMAIN OF RHODOPSIN, REFINED Deposited 2005-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 330–348（19 aa） Fragment：C-TERMINAL DOMAIN
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；278 K；Ionic strength (raw mmCIF value) 100 mM；Pressure AMBIENT
NMR sample composition 0.16 MM PURIFIED ARRESTIN, 1.77 MM 7-PHOSPHO-RH(330-348) IN SODIUM PHOSPHATE BUFFER, 10% D2O IN A TOTAL VOLUME OF 0.6 ML
Resolution not provided
2G87 Crystallographic model of bathorhodopsin Deposited 2006-03-02 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M ammonium sulfate, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.60 Å R-free 0.181
2G87 Crystallographic model of bathorhodopsin Deposited 2006-03-02 Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M ammonium sulfate, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.60 Å R-free 0.181
2HPY Crystallographic model of lumirhodopsin Deposited 2006-07-18 Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M AMMONIUM SULFATE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.80 Å R-free 0.238
2HPY Crystallographic model of lumirhodopsin Deposited 2006-07-18 Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) HG MERCURY (II) ION × 6 ZN ZINC ION × 7 RET RETINAL × 2 PLM PALMITIC ACID × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；2.9M AMMONIUM SULFATE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.80 Å R-free 0.238
2I35 Crystal structure of rhombohedral crystal form of ground-state rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 1 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 16 mM beta-mercaptoethanol, 0.4% Merpol DA, 0.1% sodium azide, equilibrated against 3.0 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 3.80 Å R-free 0.418
2I36 Crystal structure of trigonal crystal form of ground-state rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.10 Å R-free 0.412
2I36 Crystal structure of trigonal crystal form of ground-state rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.10 Å R-free 0.412
2I36 Crystal structure of trigonal crystal form of ground-state rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.10 Å R-free 0.412
2I37 Crystal structure of a photoactivated rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.15 Å R-free 0.382
2I37 Crystal structure of a photoactivated rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.15 Å R-free 0.382
2I37 Crystal structure of a photoactivated rhodopsin Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；278 K；80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Resolution 4.15 Å R-free 0.382
2J4Y Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells Deposited 2006-09-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；VAPOUR DIFFUSION IN SITTING DROPS OF 10-15 MG/ML PROTEIN AND 0.2% C8E4,0.05%LDAO AGAINST 1.1-1.7M LITHIUM SULFATE, 0.1M HEPES PH 7.5
Resolution 3.40 Å R-free 0.330
2X72 CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE. Deposited 2010-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 2 BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 4 RET RETINAL × 2 LPP 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；3.0-3.4 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 4.5
Resolution 3.00 Å R-free 0.244
3C9L Structure of ground-state bovine rhodospin in a hexagonal crystal form Deposited 2008-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Not recorded ZN ZINC ION × 1 ACE ACETYL GROUP × 1 RET RETINAL × 1 PLM PALMITIC ACID × 2 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.65 Å R-free 0.216
3C9M Structure of a mutant bovine rhodopsin in hexagonal crystal form Deposited 2008-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Mutation：N2C, D282C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACE ACETYL GROUP × 1 RET RETINAL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.40 Å R-free 0.219
3CAP Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State Deposited 2008-02-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded BGL 2-O-octyl-beta-D-glucopyranose × 6 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.266
3DQB Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；AMMONIUM SULFATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.20 Å R-free 0.248
3OAX Crystal structure of bovine rhodopsin with beta-ionone Deposited 2010-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 1 PLM PALMITIC ACID × 2 HG MERCURY (II) ION × 3 ZN ZINC ION × 4 4E6 (4E,6E)-hexadeca-1,4,6-triene × 1 HTG heptyl 1-thio-beta-D-glucopyranoside × 2 ID3 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；zinc acetate, ammonium sulfate, beta-ionone, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.60 Å R-free 0.262
3OAX Crystal structure of bovine rhodopsin with beta-ionone Deposited 2010-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 1 PLM PALMITIC ACID × 2 HG MERCURY (II) ION × 3 ZN ZINC ION × 3 4E6 (4E,6E)-hexadeca-1,4,6-triene × 1 HTG heptyl 1-thio-beta-D-glucopyranoside × 2 ID3 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 1 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；zinc acetate, ammonium sulfate, beta-ionone, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.60 Å R-free 0.262
3OAX Crystal structure of bovine rhodopsin with beta-ionone Deposited 2010-08-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 PLM PALMITIC ACID × 4 HG MERCURY (II) ION × 6 ZN ZINC ION × 7 4E6 (4E,6E)-hexadeca-1,4,6-triene × 2 HTG heptyl 1-thio-beta-D-glucopyranoside × 4 ID3 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 2 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；283 K；zinc acetate, ammonium sulfate, beta-ionone, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.60 Å R-free 0.262
3PQR Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin Deposited 2010-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded RET RETINAL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 1 SO4 SULFATE ION × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.250
3PQR Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin Deposited 2010-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Not recorded RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BOG octyl beta-D-glucopyranoside × 4 PLM PALMITIC ACID × 2 SO4 SULFATE ION × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.250
3PXO Crystal structure of Metarhodopsin II Deposited 2010-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 4 PLM PALMITIC ACID × 2 RET RETINAL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；3.0-3.4 M ammonium sulfate, 0.1 M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.245
4A4M Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin mutant in complex with a peptide resembling the C-terminus of the Galpha-protein subunit (GaCT) Deposited 2011-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 ACT ACETATE ION × 2 BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；3.0-3.4 M AMMONIUM SULPHATE, 100 MM SODIUM ACETATE PH 4.5
Resolution 3.30 Å R-free 0.262
4BEY Night blindness causing G90D rhodopsin in complex with GaCT2 peptide Deposited 2013-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 ACT ACETATE ION × 1 PLM PALMITIC ACID × 1 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.259
4BEZ Night blindness causing G90D rhodopsin in the active conformation Deposited 2013-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 2 SO4 SULFATE ION × 2 PLM PALMITIC ACID × 2 BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.30 Å R-free 0.244
4J4Q Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside Deposited 2013-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 4 PLM PALMITIC ACID × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.65 Å R-free 0.230
4PXF Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1 Deposited 2014-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 6 PLM PALMITIC ACID × 2 SO4 SULFATE ION × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；3.2 M (NH4)2SO4 in 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.75 Å R-free 0.251
4X1H Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside Deposited 2014-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BNG nonyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；3.1M ammonium sulfate, 100mM citrate
Resolution 2.29 Å R-free 0.229
5DYS Crystal Structure of T94I rhodopsin mutant Deposited 2015-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Mutation：N2C, D282C, T94I Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 1 ACT ACETATE ION × 2 BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Ammonium Sulfate, Sodium acetate
Resolution 2.30 Å R-free 0.231
5EN0 Crystal Structure of T94I rhodopsin mutant Deposited 2015-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Mutation：N2C, T94I, D282C Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 1 ACT ACETATE ION × 2 BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Ammonium sulfate, Sodium acetate
Resolution 2.81 Å R-free 0.253
5TE3 Crystal structure of Bos taurus opsin at 2.7 Angstrom Deposited 2016-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 PLM PALMITIC ACID × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；contained 2.8-3.4 M ammonium sulfate in 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Resolution 2.70 Å R-free 0.254
5TE3 Crystal structure of Bos taurus opsin at 2.7 Angstrom Deposited 2016-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 6 PLM PALMITIC ACID × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；contained 2.8-3.4 M ammonium sulfate in 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Resolution 2.70 Å R-free 0.254
5TE5 Crystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore Deposited 2016-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 7AB (2E)-{(4E)-4-[(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-ylidene]cyclohex-2-en-1-ylidene}acetaldehyde × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.8-3.4 M ammonium sulfate in 0.05-0.1 M MES, pH 6.1-6.6, or 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Resolution 4.01 Å R-free 0.357
5WKT 3.2-Angstrom In situ Mylar structure of bovine opsin at 100 K Deposited 2017-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；280 K；100 mM sodium acetate , 3.8 M (NH4)2SO4, ~12% (w/v) trehalose
Resolution 3.20 Å R-free 0.295
6FK6 Crystal structure of N2C/D282C stabilized opsin bound to RS01 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 BOG octyl beta-D-glucopyranoside × 4 DOK (2~{S})-2-(4-chlorophenyl)-3-methyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；AMMONIUM SULPHATE, SODIUM ACETATE, D(+)-TREHALOSE, PH 6.0
Resolution 2.36 Å R-free 0.226
6FK7 Crystal structure of N2C/D282C stabilized opsin bound to RS06 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 2 BOG octyl beta-D-glucopyranoside × 10 DO5 (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；AMMONIUM SULPHATE, SODIUM ACETATE, D(+)-TREHALOSE, PH 6.0
Resolution 2.62 Å R-free 0.253
6FK8 Crystal structure of N2C/D282C stabilized opsin bound to RS08 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 DNZ (2~{R},3~{S})-3-azanyl-2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one × 1 BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 2.87 Å R-free 0.247
6FK9 Crystal structure of N2C/D282C stabilized opsin bound to RS09 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 BOG octyl beta-D-glucopyranoside × 4 DNK (2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 2.63 Å R-free 0.261
6FKA Crystal structure of N2C/D282C stabilized opsin bound to RS11 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 BOG octyl beta-D-glucopyranoside × 5 DN5 (2~{S})-2-(3,4-dichlorophenyl)-3-methyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 2.70 Å R-free 0.222
6FKB Crystal structure of N2C/D282C stabilized opsin bound to RS13 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–328（328 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BMA beta-D-mannopyranose × 1 MAN alpha-D-mannopyranose × 2 BOG octyl beta-D-glucopyranoside × 5 DLH 2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 3.03 Å R-free 0.272
6FKC Crystal structure of N2C/D282C stabilized opsin bound to RS15 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 DLB 3-[1'-[(2~{S})-2-(4-chlorophenyl)-3-methyl-butanoyl]spiro[1,3-benzodioxole-2,4'-piperidine]-5-yl]propanoic acid × 1 BOG octyl beta-D-glucopyranoside × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 2.46 Å R-free 0.240
6FKD Crystal structure of N2C/D282C stabilized opsin bound to RS16 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–348（348 aa） Fragment：RESIDUES 1-326
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PLM PALMITIC ACID × 1 BOG octyl beta-D-glucopyranoside × 5 DL2 5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；see publication
Resolution 2.49 Å R-free 0.250
6FUF Crystal structure of the rhodopsin-mini-Go complex Deposited 2018-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–317（316 aa）
Not recorded RET RETINAL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M MES pH 5.5 10-20% PEG4000
Resolution 3.12 Å R-free 0.280
6NWE Crystal structure of bovine opsin with beta octyl glucoside bound Deposited 2019-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 5 PLM PALMITIC ACID × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Resolution 2.71 Å R-free 0.223
6OFJ Cryo-EM structure of the native rhodopsin dimer from rod photoreceptor cells Deposited 2019-03-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6OY9 Structure of the Rhodopsin-Transducin Complex Deposited 2019-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–348（348 aa）
Not recorded RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OYA Structure of the Rhodopsin-Transducin-Nanobody Complex Deposited 2019-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–348（348 aa）
Not recorded RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 1 second before plunging; avoid light as much as possible.
Resolution 3.30 Å
6PEL Crystal structure of bovine opsin with citronellol bound Deposited 2019-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded ODM (3R)-3,7-dimethyloct-6-en-1-ol × 1 BOG octyl beta-D-glucopyranoside × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Resolution 3.19 Å R-free 0.248
6PGS Crystal structure of bovine opsin with geraniol bound Deposited 2019-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 1 PLM PALMITIC ACID × 1 64Z Geraniol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Resolution 2.90 Å R-free 0.235
6PH7 Crystal structure of bovine opsin with nerol bound Deposited 2019-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 1 PLM PALMITIC ACID × 1 NZZ (2Z)-3,7-dimethylocta-2,6-dien-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3.1-3.3 ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Resolution 2.90 Å R-free 0.225
6PH7 Crystal structure of bovine opsin with nerol bound Deposited 2019-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 2 PLM PALMITIC ACID × 2 NZZ (2Z)-3,7-dimethylocta-2,6-dien-1-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3.1-3.3 ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Resolution 2.90 Å R-free 0.225
6QNO Rhodopsin-Gi protein complex Deposited 2019-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–348（348 aa）
Not recorded RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7MT8 Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin Deposited 2021-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–348（348 aa）
Not recorded SGV SANGIVAMYCIN × 1 RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
7MT9 Rhodopsin kinase (GRK1) in complex with rhodopsin Deposited 2021-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–348（348 aa）
Not recorded SGV SANGIVAMYCIN × 1 RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
7MTA Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab1 Deposited 2021-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–348（348 aa）
Not recorded SGV SANGIVAMYCIN × 1 RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7MTB Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab6 Deposited 2021-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–348（348 aa）
Not recorded SGV SANGIVAMYCIN × 1 RET RETINAL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZBC Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA) Deposited 2022-03-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded ACE ACETYL GROUP × 2 RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DAO LAURIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 9；294 K；36 % PEG 600, 100 mM Bicine pH 9.0
Resolution 1.80 Å R-free 0.223
7ZBE Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL) Deposited 2022-03-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded ACE ACETYL GROUP × 2 RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DAO LAURIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 9；294 K；36 % PEG 600, 100 mM Bicine pH 9.0
Resolution 1.80 Å R-free 0.247
8A6C 1 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase Deposited 2022-06-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded ACE ACETYL GROUP × 2 RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DAO LAURIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 9；294 K；36% PEG 600, 100 mM Bicine pH 9.0
Resolution 1.80 Å R-free 0.398
8A6D 10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase Deposited 2022-06-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded ACE ACETYL GROUP × 2 RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DAO LAURIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 9；294 K；36 % PEG 600, 100 mM Bicine pH 9.0
Resolution 1.80 Å R-free 0.347
8A6E 100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA) Deposited 2022-06-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DAO LAURIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PLM PALMITIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 9；294 K；36 % PEG 600, 100 mM Bicine pH 9.0
Resolution 1.80 Å R-free 0.369
8FCZ Crystal structure of ground-state rhodopsin in complex with a nanobody Deposited 2022-12-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded RET RETINAL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；30% PEG 600 0.1 M Tricine pH 8 1.2 mM F3215-0002 2% IPTG 50 mM phenol 5 mM EDTA 5 mM beta mercaptoethanol 50 mM Cyglu-4
Resolution 3.70 Å R-free 0.332
8FD0 Crystal structure of bovine rod opsin in complex with a nanobody Deposited 2022-12-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.16；277.15 K；25% PEG 600 0.1 M Tricine pH 8.16 5 mM EDTA 5 mM beta mercaptoethanol 10 mM hydroxylamine 50 mM CYGLU-4 * reservoir solution contained 30% PEG 600
Resolution 3.71 Å R-free 0.295
8FD1 Crystal structure of photoactivated rhodopsin in complex with a nanobody Deposited 2022-12-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–348（348 aa）
Chain B 1–348（348 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277.15 K；25.5% PEG 600 0.1 M Tricine pH 7.8 5 mM EDTA 5 mM beta mercaptoethanol 50 mM Cyglu-4
Resolution 4.25 Å R-free 0.295
8P12 Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13 Deposited 2023-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–348（348 aa）
Mutation：N2C, M257Y, D282C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES (pH 7.5), 100 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8P13 Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 1 Deposited 2023-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain R 1–348（348 aa）
Mutation：N2C, M257Y, D282C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES (pH 7.5), 100 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
8P15 Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 2 Deposited 2023-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain R 1–348（348 aa）
Mutation：N2C, M257Y, D282C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES (pH 7.5), 100 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9NNZ Structure of rod opsin in complex with a megabody Deposited 2025-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–348（348 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.94 Å
9NOZ Structure of photoactivated rhodopsin in complex with a megabody Deposited 2025-03-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–348（348 aa）
Chain D 1–348（348 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.48 Å
9NYX Structure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State Deposited 2025-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–322（322 aa）
Chain D 1–322（322 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) RET RETINAL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

74 other PDB entries and 94 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPSD_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–349； UniProt 1–348 Author chain B； PDBConstruct 2–349； UniProt 1–348

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2ped

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ped
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ped
Deposition date deposition_date2007-04-02
Structure title titleCrystallographic model of 9-cis-rhodopsin
Keywords keywordsRHODOPSIN, G PROTEIN-COUPLED RECEPTOR, VISUAL PIGMENT, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.66 Å
Radius of gyration Rg (electron density) rg_electron28.07 Å
Forward intensity I(0) i0100913000.00
Molecular weight molecular_weight85145.0 kDa
Excluded volume excluded_volume108360 ų
Envelope volume envelope_volume127030 ų
Hydration-shell volume shell_volume36459 ų
Envelope diameter envelope_diameter96.4 Å
Shell Rg shell_rg36.56 Å
Envelope Rg envelope_rg28.32 Å
Shape Rg shape_rg28.10 Å
Total Rg total_rg28.84 Å
Total atoms total_atoms5882
Residues n_residues696
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax96.4 Å
Rg (real space) rg_real29.52 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real1.0090e+08
I(0) uncertainty (real space) i0_real_error1.5880e+06
Rg (reciprocal space) rg_reciprocal29.58 Å
I(0) (reciprocal space) i0_reciprocal100900000.0000
Solution quality estimate total_estimate0.8966
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.6 Å
Skewness Skewness skewness0.065
Kurtosis Kurtosis kurtosis-0.665
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22380000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2peda_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.13 — Class A G protein-coupled receptor (GPCR)-like
Superfamily Superfamily superfamilyf.13.1 — Class A G protein-coupled receptor (GPCR)-like
Family Family familyf.13.1.2 — Rhodopsin-like
Domain ID domain_idd2pedb_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.13 — Class A G protein-coupled receptor (GPCR)-like
Superfamily Superfamily superfamilyf.13.1 — Class A G protein-coupled receptor (GPCR)-like
Family Family familyf.13.1.2 — Rhodopsin-like

CATH v4.4 (2 domains)

Domain ID domain_id2pedA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id2pedB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
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8. Citations (2)

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9. Files and Curves (10)