SAXSdb — 3bwq

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

Capsid protein VP1

Simian virus 40

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP1_SV40
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–272； UniProt 33–300 Author chain B； PDBConstruct 5–272； UniProt 33–300 Author chain C； PDBConstruct 5–272； UniProt 33–300 Author chain D； PDBConstruct 5–272； UniProt 33–300 Author chain E； PDBConstruct 5–272； UniProt 33–300

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	3bwq
Deposition date deposition_date	2008-01-10
Structure title title	Structure of free SV40 VP1 pentamer
Keywords keywords	;SV40, polyomavirus, ganglioside, GM1, viral receptor, virus attachment, Capsid protein, Late protein, Nucleus, Virion, VIRAL PROTEIN ;; VIRAL 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.

3bwq__assembly_1__model_1

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

Download this curve (.dat)

3bwq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bwq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.99 Å
Rg (electron density)	32.73 Å
Total Rg	33.58 Å
Atom count	10164
Residues	1319
Excluded volume	180020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bwq__assembly_1__model_1`	pentameric （5）	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 (2)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3bwqa_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.0 — automated matches

Domain ID domain_id	d3bwqb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.0 — automated matches

Domain ID domain_id	d3bwqc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.0 — automated matches

Domain ID domain_id	d3bwqd_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.0 — automated matches

Domain ID domain_id	d3bwqe_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	3bwqA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	3bwqB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	3bwqC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	3bwqD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

Domain ID domain_id	3bwqE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

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Unit-cell length a length_a	154.040 Å
Unit-cell length b length_b	93.660 Å
Unit-cell length c length_c	120.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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	39.780 Å
R factor r_factor	0.2122
R_work r_work	0.2075
R_free r_free	0.2542

Description description	Capsid protein VP1
Molecular weight formula_weight	29734.4 kDa
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	10840

Structure of free SV40 VP1 pentamer

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

Capsid protein VP1

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

3bwq__assembly_1__model_1

3bwq__assembly_1__model_1 | I(q)

3bwq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Source organism organism	Simian virus 40
NCBI taxonomy ID ncbi_taxonomy_id	10633
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	676

Structure of free SV40 VP1 pentamer

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

Capsid protein VP1

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

3bwq__assembly_1__model_1

3bwq__assembly_1__model_1 | I(q)

3bwq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)