1vpn

UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER

Method: X-RAY DIFFRACTION Dmax: 101.8 Å Quality: GOOD

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

POLYOMAVIRUS VP1 PENTAMER

Murine polyomavirus

UniProt P49302

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 32–320 Chain B; UniProt 32–320 Chain C; UniProt 32–320 Chain D; UniProt 32–320 Chain E; UniProt 32–320 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL Resolution 2.00 Å R-free 0.199
2 Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 32–320 Chain B; UniProt 32–320 Chain C; UniProt 32–320 Chain D; UniProt 32–320 Chain E; UniProt 32–320 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL Resolution 2.00 Å R-free 0.199

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COA1_POVMP
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–289; UniProt 32–320 Author chain B; PDBConstruct 1–289; UniProt 32–320 Author chain C; PDBConstruct 1–289; UniProt 32–320 Author chain D; PDBConstruct 1–289; UniProt 32–320 Author chain E; PDBConstruct 1–289; UniProt 32–320

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1vpn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vpn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vpn
Deposition date deposition_date1997-03-07
Structure title titleUNASSEMBLED POLYOMAVIRUS VP1 PENTAMER
Keywords keywordsVIRUS COAT PROTEIN, VIRUS ASSEMBLY, Viral protein; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.36
Radius of gyration Rg (electron density) rg_electron33.26
Forward intensity I(0) i0385701000.00
Molecular weight molecular_weight158270.0 kDa
Excluded volume excluded_volume197970 ų
Envelope volume envelope_volume251010 ų
Hydration-shell volume shell_volume58770 ų
Envelope diameter envelope_diameter105.1
Shell Rg shell_rg42.94
Envelope Rg envelope_rg33.12
Shape Rg shape_rg33.19
Total Rg total_rg34.18
Total atoms total_atoms11134
Residues n_residues1429
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax101.8
Rg (real space) rg_real34.10
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real3.8570e+08
I(0) uncertainty (real space) i0_real_error6.4320e+06
Rg (reciprocal space) rg_reciprocal34.26
I(0) (reciprocal space) i0_reciprocal385800000.0000
Solution quality estimate total_estimate0.8989
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7
Skewness Skewness skewness0.006
Kurtosis Kurtosis kurtosis-0.538
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha95480000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.908

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1vpna_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1vpnb_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1vpnc_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1vpnd_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP
Domain ID domain_idd1vpne_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.6 — Group I dsDNA viruses
Family Family familyb.121.6.1 — Papovaviridae-like VP

CATH v4.4 (5 domains)

Domain ID domain_id1vpnA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1vpnB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1vpnC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1vpnD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus
Domain ID domain_id1vpnE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily10 — Capsid protein VP1,Polyomavirus

8. Citations (4)

9. Files and Curves (10)