← Back to search
1c8d

CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE

Method: X-RAY DIFFRACTION Dmax: 103.9 Å Quality: GOOD
▼

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

CANINE PARVOVIRUS CAPSID

OrganismNot specified

UniProt P30129

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 × 60 PDB declaration: complete icosahedral assembly（60） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 60 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å
4 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å
6 Protein homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count Chain A； UniProt 1–584 Not recorded CA CALCIUM ION × 60 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.00 Å

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.

Other PDB Difference from Current Entry 1C8D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 60 PDB declaration: 180-MERIC
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Homooligomer；Protein × 5 PDB declaration: pentadecameric
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octadecameric
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1IJS CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C Deposited 1996-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Homooligomer；Protein × 60 PDB declaration: 180-meric
Chain P 1–584（584 aa）
Mutation：A300D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Resolution 3.25 Å
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: complete icosahedral assembly
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253
1P5Y The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants Deposited 2003-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 37–584（548 aa） Fragment：SEQUENCE DATABASE RESIDUES 190-737
Mutation：N93D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.253

2 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COAT_PAVC2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–584； UniProt 1–584

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 1c8d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c8d
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1c8d
Deposition date deposition_date2000-05-05
Structure title titleCANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE
Keywords keywordsCapsid, canine parvovirus, strain D, empty capsid, A300D, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.49 Å
Radius of gyration Rg (electron density) rg_electron28.78 Å
Forward intensity I(0) i063581500.00
Molecular weight molecular_weight61602.0 kDa
Excluded volume excluded_volume76680 ų
Envelope volume envelope_volume108610 ų
Hydration-shell volume shell_volume32499 ų
Envelope diameter envelope_diameter110.6 Å
Shell Rg shell_rg34.64 Å
Envelope Rg envelope_rg29.28 Å
Shape Rg shape_rg28.74 Å
Total Rg total_rg29.52 Å
Total atoms total_atoms4353
Residues n_residues548
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax103.9 Å
Rg (real space) rg_real29.59 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real6.3580e+07
I(0) uncertainty (real space) i0_real_error9.8960e+05
Rg (reciprocal space) rg_reciprocal29.55 Å
I(0) (reciprocal space) i0_reciprocal63580000.0000
Solution quality estimate total_estimate0.8560
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.7 Å
Skewness Skewness skewness0.519
Kurtosis Kurtosis kurtosis0.106
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7027000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.937
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1c8da_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.2 — Parvoviridae-like VP

CATH v4.4 (1 domains)

Domain ID domain_id1c8dA00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily10 — Parvovirus coat protein VP1/VP2
▶

8. Citations (5)

▶

9. Files and Curves (10)