1pvc

REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 97.0 Å Quality: GOOD

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

POLIOVIRUS TYPE 3, SABIN STRAIN

OrganismNot specified

UniProt P03302

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 heterocomplex Heteromer Protein × 300 PDB declaration: 300-MERIC(300) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 60 POLIOVIRUS TYPE 3, SABIN STRAIN × 60 POLIOVIRUS TYPE 3, SABIN STRAIN × 60 SPH SPHINGOSINE × 60 MYR MYRISTIC ACID × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 1 POLIOVIRUS TYPE 3, SABIN STRAIN × 1 POLIOVIRUS TYPE 3, SABIN STRAIN × 1 SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 5 POLIOVIRUS TYPE 3, SABIN STRAIN × 5 POLIOVIRUS TYPE 3, SABIN STRAIN × 5 SPH SPHINGOSINE × 5 MYR MYRISTIC ACID × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 6 POLIOVIRUS TYPE 3, SABIN STRAIN × 6 POLIOVIRUS TYPE 3, SABIN STRAIN × 6 SPH SPHINGOSINE × 6 MYR MYRISTIC ACID × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 1 POLIOVIRUS TYPE 3, SABIN STRAIN × 1 POLIOVIRUS TYPE 3, SABIN STRAIN × 1 SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
6 Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric(75) Consistent with protein copy count Chain 2; UniProt 70–340 Chain 4; UniProt 2–69 Not recorded POLIOVIRUS TYPE 3, SABIN STRAIN × 15 POLIOVIRUS TYPE 3, SABIN STRAIN × 15 POLIOVIRUS TYPE 3, SABIN STRAIN × 15 SPH SPHINGOSINE × 15 MYR MYRISTIC ACID × 15 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 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.

11 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL3L
Isoform
PDB entities 3, 5
Chains and sequence ranges Author chain 2; PDBConstruct 1–271; UniProt 70–340 Author chain 4; PDBConstruct 1–68; UniProt 2–69

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 1pvc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pvc
Deposition date deposition_date1995-03-30
Structure title titleREFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION
Keywords keywordsVIRUS, Icosahedral virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.05
Radius of gyration Rg (electron density) rg_electron29.05
Forward intensity I(0) i0141935000.00
Molecular weight molecular_weight94482.0 kDa
Excluded volume excluded_volume118230 ų
Envelope volume envelope_volume147860 ų
Hydration-shell volume shell_volume41285 ų
Envelope diameter envelope_diameter101.9
Shell Rg shell_rg37.11
Envelope Rg envelope_rg29.68
Shape Rg shape_rg29.03
Total Rg total_rg29.85
Total atoms total_atoms6652
Residues n_residues846
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 dmax97.0
Rg (real space) rg_real29.97
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real1.4190e+08
I(0) uncertainty (real space) i0_real_error1.9160e+06
Rg (reciprocal space) rg_reciprocal30.00
I(0) (reciprocal space) i0_reciprocal141900000.0000
Solution quality estimate total_estimate0.8935
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.6
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.344
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27790000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.955

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1pvc.1
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1pvc1_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1pvc3_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

Domain ID domain_id1pvc100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1pvc200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1pvc300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1pvc400
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4

8. Citations (8)

9. Files and Curves (10)