9yhc

Crystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)

Method: X-RAY DIFFRACTION Dmax: 102.0 Å Quality: GOOD

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:D31H EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.35 Å R-free 0.172
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1334–1493 Fragment:macrodomain Mutation:D31H EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.35 Å R-free 0.172
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1334–1493 Fragment:macrodomain Mutation:D31H EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.35 Å R-free 0.172
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1334–1493 Fragment:macrodomain Mutation:D31H EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;292 K;0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350 Resolution 1.35 Å R-free 0.172

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 9yhc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9yhc
Deposition date deposition_date2025-09-30
最后修订 last_revision2025-11-26
Structure title titleCrystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)
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_guinier30.72
Radius of gyration Rg (electron density) rg_electron29.88
Forward intensity I(0) i093979100.00
Molecular weight molecular_weight73389.0 kDa
Excluded volume excluded_volume90653 ų
Envelope volume envelope_volume119340 ų
Hydration-shell volume shell_volume34042 ų
Envelope diameter envelope_diameter110.6
Shell Rg shell_rg36.27
Envelope Rg envelope_rg29.57
Shape Rg shape_rg29.90
Total Rg total_rg30.42
Total atoms total_atoms10165
Residues n_residues657
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 dmax102.0
Rg (real space) rg_real30.67
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real9.3980e+07
I(0) uncertainty (real space) i0_real_error1.5910e+06
Rg (reciprocal space) rg_reciprocal30.69
I(0) (reciprocal space) i0_reciprocal93980000.0000
Solution quality estimate total_estimate0.8112
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary41.2
Skewness Skewness skewness0.241
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26260000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)