9yhd

Crystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P41 crystal form) in complex with ADP-ribose

Method: X-RAY DIFFRACTION Dmax: 90.6 Å Quality: EXCELLENT

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

Non-structural protein 3

Chikungunya virus

UniProt Q8JUX6

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.81 Å R-free 0.249
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.81 Å R-free 0.249
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.81 Å R-free 0.249
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.81 Å R-free 0.249

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.

163 other PDB entries and 601 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLN_CHIKS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–168; UniProt 1334–1493 Author chain B; PDBConstruct 9–168; UniProt 1334–1493 Author chain C; PDBConstruct 9–168; UniProt 1334–1493 Author chain D; PDBConstruct 9–168; UniProt 1334–1493

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 9yhd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9yhd
Deposition date deposition_date2025-09-30
最后修订 last_revision2025-11-26
Structure title titleCrystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P41 crystal form) in complex with ADP-ribose
Keywords keywordsChikungunya virus, ADP-ribose, AViDD, Advanced Light Source 8.3.1, VIRAL PROTEIN, HYDROLASE; VIRAL PROTEIN,HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.68
Radius of gyration Rg (electron density) rg_electron28.96
Forward intensity I(0) i085514800.00
Molecular weight molecular_weight70587.0 kDa
Excluded volume excluded_volume87464 ų
Envelope volume envelope_volume109450 ų
Hydration-shell volume shell_volume32246 ų
Envelope diameter envelope_diameter96.0
Shell Rg shell_rg35.46
Envelope Rg envelope_rg28.76
Shape Rg shape_rg28.94
Total Rg total_rg29.62
Total atoms total_atoms9837
Residues n_residues640
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 dmax90.6
Rg (real space) rg_real29.60
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real8.5510e+07
I(0) uncertainty (real space) i0_real_error1.2110e+06
Rg (reciprocal space) rg_reciprocal29.64
I(0) (reciprocal space) i0_reciprocal85520000.0000
Solution quality estimate total_estimate0.9079
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary42.8
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37210000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.908

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)