Rhodopsin
OrganismNot specified
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 Heteromer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 1–348 Chain B； UniProt 1–348 | Not recorded | Nanobody Nb2 × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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 × 1 | 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 |
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 8FD0 | 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 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 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 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 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 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 | 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 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 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）
|
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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）
|
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 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）
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 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）
|
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 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）
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 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 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 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 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 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 |
| 2PED Crystallographic model of 9-cis-rhodopsin Deposited 2007-04-02 | 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）
|
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 2.95 Å R-free 0.289 |
| 2PED Crystallographic model of 9-cis-rhodopsin Deposited 2007-04-02 | 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）
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 2.95 Å R-free 0.289 |
| 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 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 | 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 mutation/modification Different oligomeric state 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 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 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）
|
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 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 oligomeric state 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 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 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 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 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 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）
|
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 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 |
| 8FD1 Crystal structure of photoactivated rhodopsin in complex with a nanobody Deposited 2022-12-01 | 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 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 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 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 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 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 mutation/modification 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 95 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 1–348； UniProt 1–348 Author chain B； PDBConstruct 1–348； UniProt 1–348 |
