SAXSdb — 3j9s

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

Intermediate capsid protein VP6

Bovine rotavirus strain UK/G6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 3 CHLORIDE ION × 3 CALCIUM ION × 6 water × 3	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 CALCIUM ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 CALCIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP6_ROTRF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–398； UniProt 1–397

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	3j9s
Deposition date deposition_date	2015-02-19
Structure title title	Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution
Keywords keywords	rotavirus, virus, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

3j9s__assembly_1__model_1

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

Download this curve (.dat)

3j9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.45 Å
Rg (electron density)	31.52 Å
Total Rg	32.06 Å
Atom count	9498
Residues	1191
Excluded volume	168790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j9s__assembly_1__model_1`	3-MERIC （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3j9s__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3j9s__assembly_3__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Intermediate capsid protein VP6
Molecular weight formula_weight	44905.7 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	3271

XMDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLIKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVITSADGATTWYFNPVILRPNNVEIEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Source Source

Source organism organism	Bovine rotavirus strain UK/G6
NCBI taxonomy ID ncbi_taxonomy_id	10934
Host organism host_organism	Chlorocebus sabaeus

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

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

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3j9sa1
Class class	a — All alpha proteins
Fold Fold fold	a.115 — A virus capsid protein alpha-helical domain
Superfamily Superfamily superfamily	a.115.1 — A virus capsid protein alpha-helical domain
Family Family family	a.115.1.2 — vp6, the major capsid protein of group A rotavirus

Domain ID domain_id	d3j9sa2
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.1 — Top domain of virus capsid protein

CATH v4.4 (2 domains)

Domain ID domain_id	3j9sA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3j9sA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.60 Å
Resolution测定Method resolution_method	projection matching
颗粒数 num_particles	4000

Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution

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

Intermediate capsid protein VP6

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

3j9s__assembly_1__model_1

3j9s__assembly_1__model_1 | I(q)

3j9s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution

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

Intermediate capsid protein VP6

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

3j9s__assembly_1__model_1

3j9s__assembly_1__model_1 | I(q)

3j9s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)