SAXSdb — 3bwr

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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	Other combination	Homooligomer	Protein 5 其他Polymer 3	;beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose ; × 3 1,2-ETHANEDIOL × 6 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	3bwr
Deposition date deposition_date	2008-01-10
Structure title title	SV40 VP1 pentamer in complex with GM1 oligosaccharide
Keywords keywords	;SV40, GM1, viral receptor, viral attachment, ganglioside, VP1, polyomaviruses, 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.

3bwr__assembly_1__model_1

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

Download this curve (.dat)

3bwr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bwr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.70 Å
Rg (electron density)	32.47 Å
Total Rg	33.32 Å
Atom count	10382
Residues	1318
Excluded volume	183990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bwr__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 (4)

Entity 1 Entity 1 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	11292

GSHMGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKN

Source Source

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

Entity 2 Entity 2 branched

Description description	;beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	998.9 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	855

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3bwra_
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	d3bwrb_
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	d3bwrc_
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	d3bwrd_
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	d3bwre_
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	3bwrA00
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	3bwrB00
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	3bwrC00
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	3bwrD00
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	3bwrE00
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	152.764 Å
Unit-cell length b length_b	93.087 Å
Unit-cell length c length_c	118.882 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.60 °
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	2.250 Å
Low-resolution limit resolution_low	29.760 Å
R factor r_factor	0.1921
R_work r_work	0.1874
R_free r_free	0.2332

SV40 VP1 pentamer in complex with GM1 oligosaccharide

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

3bwr__assembly_1__model_1

3bwr__assembly_1__model_1 | I(q)

3bwr__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

SV40 VP1 pentamer in complex with GM1 oligosaccharide

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

3bwr__assembly_1__model_1

3bwr__assembly_1__model_1 | I(q)

3bwr__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)