3oax

Crystal structure of bovine rhodopsin with beta-ionone

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Rhodopsin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 2	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 RETINAL × 1 PALMITIC ACID × 2 MERCURY (II) ION × 3 ZINC ION × 4 (4E,6E)-hexadeca-1,4,6-triene × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-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 RETINAL × 1 PALMITIC ACID × 2 MERCURY (II) ION × 3 ZINC ION × 3 (4E,6E)-hexadeca-1,4,6-triene × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 1 HEPTANE-1,2,3-TRIOL × 1 water × 1	Consistent with protein count
3	Other combination	Homooligomer	Protein 2 其他Polymer 4	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 × 2 ;alpha-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 RETINAL × 2 PALMITIC ACID × 4 MERCURY (II) ION × 6 ZINC ION × 7 (4E,6E)-hexadeca-1,4,6-triene × 2 heptyl 1-thio-beta-D-glucopyranoside × 4 (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one × 2 HEPTANE-1,2,3-TRIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3oax
Deposition date deposition_date	2010-08-05
Structure title title	Crystal structure of bovine rhodopsin with beta-ionone
Keywords keywords	7TM, Signaling protein; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3oax__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3oax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oax__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.01 Å
Rg (electron density)	22.80 Å
Total Rg	23.72 Å
Atom count	2945
Residues	348
Excluded volume	54297 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oax__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oax__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3oax__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Rhodopsin
Molecular weight formula_weight	39057.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6015

XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	;alpha-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 ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	RETINAL
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 non-polymer

Description description	(4E,6E)-hexadeca-1,4,6-triene
Molecular weight formula_weight	220.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	heptyl 1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	294.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one
Molecular weight formula_weight	192.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	HEPTANE-1,2,3-TRIOL
Molecular weight formula_weight	148.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3oaxa_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.13 — Class A G protein-coupled receptor (GPCR)-like
Superfamily Superfamily superfamily	f.13.1 — Class A G protein-coupled receptor (GPCR)-like
Family Family family	f.13.1.2 — Rhodopsin-like

Domain ID domain_id	d3oaxb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.13 — Class A G protein-coupled receptor (GPCR)-like
Superfamily Superfamily superfamily	f.13.1 — Class A G protein-coupled receptor (GPCR)-like
Family Family family	f.13.1.2 — Rhodopsin-like

CATH v4.4 (2 domains)

Domain ID domain_id	3oaxA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

Domain ID domain_id	3oaxB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

▶

Unit-cell length a length_a	96.990 Å
Unit-cell length b length_b	96.990 Å
Unit-cell length c length_c	149.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2620

Crystal structure of bovine rhodopsin with beta-ionone

1. Protein Identity and Related Structures Protein Identity & Related Structures

Rhodopsin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3oax__assembly_1__model_1

3oax__assembly_1__model_1 | I(q)

3oax__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of bovine rhodopsin with beta-ionone

1. Protein Identity and Related Structures Protein Identity & Related Structures

Rhodopsin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3oax__assembly_1__model_1

3oax__assembly_1__model_1 | I(q)

3oax__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)