3vvk

An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

Method: X-RAY DIFFRACTION

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

Halorhodopsin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	RETINAL × 3 nonyl beta-D-glucopyranoside × 3 BACTERIORUBERIN × 1 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	RETINAL × 3 nonyl beta-D-glucopyranoside × 1 BACTERIORUBERIN × 1 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE × 2 AZIDE ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3ITX1_NATPD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–291； UniProt 1–291 Author chain B； PDBConstruct 1–291； UniProt 1–291 Author chain C； PDBConstruct 1–291； UniProt 1–291 Author chain D； PDBConstruct 1–291； UniProt 1–291 Author chain E； PDBConstruct 1–291； UniProt 1–291 Author chain F； PDBConstruct 1–291； UniProt 1–291

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	3vvk
Deposition date deposition_date	2012-07-26
Structure title title	An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin
Keywords keywords	;seven-transmembrane-retinylidene protein, chloride-bound purple form, light-driven chloride ion pump, azide-bound purple form, light-driven proton pump, MEMBRANE PROTEIN ;; MEMBRANE 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.

3vvk__assembly_1__model_1

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

Download this curve (.dat)

3vvk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vvk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.24 Å
Rg (electron density)	25.62 Å
Total Rg	26.64 Å
Atom count	6070
Residues	778
Excluded volume	112480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vvk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vvk__assembly_2__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	Halorhodopsin
Molecular weight formula_weight	30975.1 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12401

MTETLPPVTESAVALQAEVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGSILDVPSASGAPADD

Entity 2 Entity 2 non-polymer

Description description	RETINAL
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	nonyl beta-D-glucopyranoside
Molecular weight formula_weight	306.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	BACTERIORUBERIN
Molecular weight formula_weight	741.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
Molecular weight formula_weight	885.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	285

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3vvka_
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.13.1.0 — automated matches

Domain ID domain_id	d3vvkb_
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.13.1.0 — automated matches

Domain ID domain_id	d3vvkc_
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.13.1.0 — automated matches

Domain ID domain_id	d3vvkd_
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.13.1.0 — automated matches

Domain ID domain_id	d3vvke_
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.13.1.0 — automated matches

Domain ID domain_id	d3vvkf_
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.13.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3vvkA00
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	3vvkB00
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	3vvkC00
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	3vvkD00
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	3vvkE00
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	3vvkF00
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	153.850 Å
Unit-cell length b length_b	97.900 Å
Unit-cell length c length_c	101.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2109
R_free r_free	0.2400

An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

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

Halorhodopsin

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

3vvk__assembly_1__model_1

3vvk__assembly_1__model_1 | I(q)

3vvk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

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

Halorhodopsin

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

3vvk__assembly_1__model_1

3vvk__assembly_1__model_1 | I(q)

3vvk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)