9vmd

HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation2 splitRNA

Method: ELECTRON MICROSCOPY Dmax: 99.3 Å Quality: REASONABLE

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

Protease 3C

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–RNA Heteromer Protein × 3 RNA 1 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain O; UniProt 1539–1718 Not recorded YDF heavy chain × 1 YDF light chain × 1 RNA (83-MER) × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 4.38 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
Chains and sequence ranges Author chain O; PDBConstruct 1–180; UniProt 1539–1718

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 9vmd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9vmd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9vmd
Deposition date deposition_date2025-06-27
Structure title titleHRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation2 splitRNA
Keywords keywordscloverleafRNA, 3c, complex, RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA, RNA BINDING PROTEIN-IMMUNE SYSTEM-RNA complex; RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier30.57
Radius of gyration Rg (electron density) rg_electron29.38
Forward intensity I(0) i0121816000.00
Molecular weight molecular_weight68985.0 kDa
Excluded volume excluded_volume78480 ų
Envelope volume envelope_volume114180 ų
Hydration-shell volume shell_volume33307 ų
Envelope diameter envelope_diameter106.2
Shell Rg shell_rg35.50
Envelope Rg envelope_rg28.90
Shape Rg shape_rg29.29
Total Rg total_rg30.09
Total atoms total_atoms4743
Residues n_residues489
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 dmax99.3
Rg (real space) rg_real30.46
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real1.2180e+08
I(0) uncertainty (real space) i0_real_error1.5840e+06
Rg (reciprocal space) rg_reciprocal30.51
I(0) (reciprocal space) i0_reciprocal121800000.0000
Solution quality estimate total_estimate0.7115
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.384
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5128000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 1.000; Smooth: 0.966

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)