SAXSdb — 5cpz

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

Capsid protein VP1

Murine polyomavirus (strain P16 small-plaque)

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 5	;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ; × 5 SULFATE ION × 14 GLYCEROL × 20 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP1_POVMP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 34–317 Author chain B； PDBConstruct 1–284； UniProt 34–317 Author chain C； PDBConstruct 1–284； UniProt 34–317 Author chain D； PDBConstruct 1–284； UniProt 34–317 Author chain E； PDBConstruct 1–284； UniProt 34–317

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	5cpz
Deposition date deposition_date	2015-07-21
Structure title title	Crystal structure of murine polyomavirus RA strain VP1 in complex with the GT1a glycan
Keywords keywords	Murine Polyomavirus, Virus protein, carbohydrate complex, virus-host interaction, 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.

5cpz__assembly_1__model_1

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

Download this curve (.dat)

5cpz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cpz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.34 Å
Rg (electron density)	33.24 Å
Total Rg	34.19 Å
Atom count	11456
Residues	1402
Excluded volume	203480 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	31558.7 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	13767

GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK

Source Source

Source organism organism	Murine polyomavirus (strain P16 small-plaque)
Common name common_name	MPyV
NCBI taxonomy ID ncbi_taxonomy_id	47935
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ;
Molecular weight formula_weight	1128.0 kDa
Source method src_method	man
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1885

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5cpza_
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.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cpzb_
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.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cpzc_
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.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cpzd_
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.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5cpze_
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.121.6.1 — Papovaviridae-like VP

CATH v4.4 (5 domains)

Domain ID domain_id	5cpzA00
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	5cpzB00
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	5cpzC00
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	5cpzD00
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	5cpzE00
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	219.550 Å
Unit-cell length b length_b	219.550 Å
Unit-cell length c length_c	99.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	30

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	48.220 Å
R factor r_factor	0.1554
R_work r_work	0.1549
R_free r_free	0.1724

Crystal structure of murine polyomavirus RA strain VP1 in complex with the GT1a glycan

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

5cpz__assembly_1__model_1

5cpz__assembly_1__model_1 | I(q)

5cpz__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of murine polyomavirus RA strain VP1 in complex with the GT1a glycan

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

5cpz__assembly_1__model_1

5cpz__assembly_1__model_1 | I(q)

5cpz__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)