SAXSdb — 5jjf

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

Sensory rhodopsin-2

Natronomonas pharaonis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Sensory rhodopsin II transducer × 2 （P42259） RETINAL × 2 octyl beta-D-glucopyranoside × 2 EICOSANE × 24 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BACS2_NATPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 2–239

Sensory rhodopsin II transducer

Natronomonas pharaonis

UniProt P42259

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Sensory rhodopsin-2 × 2 （P42196） RETINAL × 2 octyl beta-D-glucopyranoside × 2 EICOSANE × 24 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HTR2_NATPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–154； UniProt 5–157

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	5jjf
Deposition date deposition_date	2016-04-23
Structure title title	Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) - M state
Keywords keywords	sensory rhodopsin II, transducer, membrane protein complex, signaling protein; 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.

5jjf__assembly_1__model_1

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

Download this curve (.dat)

5jjf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jjf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	— Å
Rg (electron density)	26.57 Å
Total Rg	102.20 Å
Atom count	302
Residues	0
Excluded volume	7936 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jjf__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Sensory rhodopsin-2
Molecular weight formula_weight	26534.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4481

VGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGESLAGVDTDAPAVADENSHHHHHHH

Source Source

Source organism organism	Natronomonas pharaonis
Common name common_name	Natronobacterium pharaonis
NCBI taxonomy ID ncbi_taxonomy_id	2257
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Sensory rhodopsin II transducer
Molecular weight formula_weight	17224.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AVSRLLLPSRVRHSYTGKMGAVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVAATLGGDTAASLSTLAAKASRMGDGDLDVELETRREDEIGDLYAAFDEMRQSVRTSLEDAKNAREDAEQAQKRAEEINTNSHHHHHHH

Source Source

Source organism organism	Natronomonas pharaonis
Common name common_name	Natronobacterium pharaonis
NCBI taxonomy ID ncbi_taxonomy_id	2257
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	RETINAL
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	EICOSANE
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5jjfa_
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.13.1.1 — Bacteriorhodopsin-like

Domain ID domain_id	d5jjfb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.4 — Htr2 transmembrane domain-like
Family Family family	f.17.4.1 — Htr2 transmembrane domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	5jjfA00
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	5jjfB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	470 — Helix hairpin bin

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Unit-cell length a length_a	49.558 Å
Unit-cell length b length_b	113.779 Å
Unit-cell length c length_c	125.387 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.000 Å
R factor r_factor	0.2031
R_work r_work	0.2015
R_free r_free	0.2324

Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) - M state

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

Sensory rhodopsin-2

State in the Current Structure

Other States of the Same Protein in the Database

Sensory rhodopsin II transducer

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

5jjf__assembly_1__model_1

5jjf__assembly_1__model_1 | I(q)

5jjf__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) - M state

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

Sensory rhodopsin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sensory rhodopsin II transducer

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

5jjf__assembly_1__model_1

5jjf__assembly_1__model_1 | I(q)

5jjf__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)