3pqr

Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin

Method: X-RAY DIFFRACTION

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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	Heteromer	Protein 2 其他Polymer 2	Guanine nucleotide-binding protein G(t) subunit alpha-1 × 1 （P04695） ;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 alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 1 RETINAL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 octyl beta-D-glucopyranoside × 2 PALMITIC ACID × 1 SULFATE ION × 1 ACETATE ION × 2 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 4	Guanine nucleotide-binding protein G(t) subunit alpha-1 × 2 （P04695） ;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 ; × 2 alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 2 RETINAL × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 octyl beta-D-glucopyranoside × 4 PALMITIC ACID × 2 SULFATE ION × 2 ACETATE ION × 4 water × 4	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 1–348； UniProt 1–348

Guanine nucleotide-binding protein G(t) subunit alpha-1

OrganismNot specified

UniProt P04695

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 2	Rhodopsin × 1 （P02699） ;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 alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 1 RETINAL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 octyl beta-D-glucopyranoside × 2 PALMITIC ACID × 1 SULFATE ION × 1 ACETATE ION × 2 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 4	Rhodopsin × 2 （P02699） ;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 ; × 2 alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 2 RETINAL × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 octyl beta-D-glucopyranoside × 4 PALMITIC ACID × 2 SULFATE ION × 2 ACETATE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNAT1_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 340–350

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3pqr
Deposition date deposition_date	2010-11-26
Structure title title	Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin
Keywords keywords	;protein, retinal protein, photoreceptor, active state, chromophore, G-protein coupled receptor, glycoprotein, lipoprotein, palmitate, phosphoprotein, photoreceptor protein, sensory transduction, transducer, transmembrane, vision, signaling protein, G-protein, transducin, Galpha subunit, membrane, receptor, GTP-binding, myristate, nucleotide-binding, G-protein-coupled receptor, rhodopsin, opsin ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3pqr__assembly_1__model_1

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

Download this curve (.dat)

3pqr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pqr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.92 Å
Rg (electron density)	22.68 Å
Total Rg	23.74 Å
Atom count	2858
Residues	337
Excluded volume	52378 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pqr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pqr__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Rhodopsin
Molecular weight formula_weight	39031.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2904

MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Entity 2 Entity 2 polymer

Description description	Guanine nucleotide-binding protein G(t) subunit alpha-1
Molecular weight formula_weight	1261.5 kDa
Mutation mutation	K341L,C347V
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ILENLKDVGLF

Entity 3 Entity 3 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 4 Entity 4 branched

Description description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 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	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3pqra_
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 (1 domains)

Domain ID domain_id	3pqrA00
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

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Unit-cell length a length_a	241.550 Å
Unit-cell length b length_b	241.550 Å
Unit-cell length c length_c	109.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	34.860 Å
R factor r_factor	—
R_work r_work	0.2173
R_free r_free	0.2496

Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin

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

Guanine nucleotide-binding protein G(t) subunit alpha-1

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

3pqr__assembly_1__model_1

3pqr__assembly_1__model_1 | I(q)

3pqr__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin

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

Guanine nucleotide-binding protein G(t) subunit alpha-1

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

3pqr__assembly_1__model_1

3pqr__assembly_1__model_1 | I(q)

3pqr__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)