1r08

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

Method: X-RAY DIFFRACTION Dmax: 95.6 Å Quality: GOOD

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

HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)

Human rhinovirus 14

UniProt P03303

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 × 240 PDB declaration: 240-MERIC(240) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
3 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
4 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
6 Protein homooligomer Homooligomer Protein × 80 PDB declaration: 80-meric(80) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded W42 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE × 20 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions 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.

58 other PDB entries and 235 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain 1; PDBConstruct 1–289; UniProt 567–855 Author chain 2; PDBConstruct 1–262; UniProt 69–330 Author chain 3; PDBConstruct 1–236; UniProt 331–566 Author chain 4; PDBConstruct 1–68; UniProt 1–68

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 1r08

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1r08
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1r08
Deposition date deposition_date1988-10-03
Structure title titleSTRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES
Keywords keywordsRHINOVIRUS COAT PROTEIN, 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_guinier29.62
Radius of gyration Rg (electron density) rg_electron28.58
Forward intensity I(0) i0126516000.00
Molecular weight molecular_weight89458.0 kDa
Excluded volume excluded_volume112070 ų
Envelope volume envelope_volume137010 ų
Hydration-shell volume shell_volume39279 ų
Envelope diameter envelope_diameter102.3
Shell Rg shell_rg36.37
Envelope Rg envelope_rg29.28
Shape Rg shape_rg28.59
Total Rg total_rg29.25
Total atoms total_atoms6299
Residues n_residues804
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 dmax95.6
Rg (real space) rg_real29.59
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real1.2650e+08
I(0) uncertainty (real space) i0_real_error1.9230e+06
Rg (reciprocal space) rg_reciprocal29.61
I(0) (reciprocal space) i0_reciprocal126500000.0000
Solution quality estimate total_estimate0.8896
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.363
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24400000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.908

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1r08.1
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_idd1r081_
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_idd1r083_
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_id1r08100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1r08200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1r08300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1r08400
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4

8. Citations (13)

9. Files and Curves (10)