8pnb

HRV empty capsid

Method: ELECTRON MICROSCOPY Dmax: 100.4 Å Quality: GOOD

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

Capsid protein VP1

rhinovirus B14

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 × 180 PDB declaration: trimeric(180) Consistent with protein copy count Chain 1; UniProt 627–856 Chain 2; UniProt 76–331 Chain 3; UniProt 332–567 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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 240 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 1, 2, 3
Chains and sequence ranges Author chain 1; PDBConstruct 1–230; UniProt 627–856 Author chain 2; PDBConstruct 1–256; UniProt 76–331 Author chain 3; PDBConstruct 1–236; UniProt 332–567

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 8pnb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8pnb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8pnb
Deposition date deposition_date2023-06-30
Structure title titleHRV empty capsid
Keywords keywordscryo-EM, HRV-B14, SsRNA virus, capsid, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier29.97
Radius of gyration Rg (electron density) rg_electron28.99
Forward intensity I(0) i0102327000.00
Molecular weight molecular_weight80238.0 kDa
Excluded volume excluded_volume100570 ų
Envelope volume envelope_volume128230 ų
Hydration-shell volume shell_volume37081 ų
Envelope diameter envelope_diameter104.9
Shell Rg shell_rg35.95
Envelope Rg envelope_rg29.45
Shape Rg shape_rg28.99
Total Rg total_rg29.66
Total atoms total_atoms5656
Residues n_residues722
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 dmax100.4
Rg (real space) rg_real29.97
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real1.0230e+08
I(0) uncertainty (real space) i0_real_error1.4310e+06
Rg (reciprocal space) rg_reciprocal29.97
I(0) (reciprocal space) i0_reciprocal102300000.0000
Solution quality estimate total_estimate0.8868
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary98.5
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.303
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha28730000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)