4qry

the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion

Method: X-RAY DIFFRACTION

▼

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 BROMIDE ION × 6 nonyl beta-D-glucopyranoside × 2 2,3-DI-PHYTANYL-GLYCEROL × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	RETINAL × 3 BROMIDE ION × 6 nonyl beta-D-glucopyranoside × 3 2,3-DI-PHYTANYL-GLYCEROL × 5 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 E； PDBConstruct 1–291； UniProt 1–291 Author chain F； PDBConstruct 1–291； UniProt 1–291 Author chain G； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4qry
Deposition date deposition_date	2014-07-02
Structure title title	the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion
Keywords keywords	7 transmembrane helices, light-driven chloride ion pump, retinal bacterioruberin, membrane, MEMBRANE PROTEIN; MEMBRANE 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.

4qry__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4qry__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qry__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.38 Å
Rg (electron density)	21.86 Å
Total Rg	23.37 Å
Atom count	163
Residues	0
Excluded volume	4055 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qry__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qry__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

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,E,F,G
Atom count atom_count	12404

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	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	nonyl beta-D-glucopyranoside
Molecular weight formula_weight	306.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	2,3-DI-PHYTANYL-GLYCEROL
Molecular weight formula_weight	653.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4qrya_
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	d4qryb_
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	d4qryc_
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	d4qrye_
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	d4qryf_
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	d4qryg_
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	4qryA00
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	4qryB00
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	4qryC00
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	4qryE00
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	4qryF00
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	4qryG00
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	153.360 Å
Unit-cell length b length_b	98.300 Å
Unit-cell length c length_c	100.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.13 °
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	2.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2428

the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion

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

4qry__assembly_2__model_1

4qry__assembly_2__model_1 | I(q)

4qry__assembly_2__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion

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

4qry__assembly_2__model_1

4qry__assembly_2__model_1 | I(q)

4qry__assembly_2__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)