9yhe

Crystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P31 crystal form)

Method: X-RAY DIFFRACTION Dmax: 101.5 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:D31N EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292 K;0.1 M Calcium chloride dihydrate, 20% (w/v) PEG 6000, 10% (v/v) Ethylene glycol Resolution 1.35 Å R-free 0.166
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292 K;0.1 M Calcium chloride dihydrate, 20% (w/v) PEG 6000, 10% (v/v) Ethylene glycol Resolution 1.35 Å R-free 0.166
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292 K;0.1 M Calcium chloride dihydrate, 20% (w/v) PEG 6000, 10% (v/v) Ethylene glycol Resolution 1.35 Å R-free 0.166
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1334–1493 Fragment:macrodomain Mutation:D31N EDO 1,2-ETHANEDIOL × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292 K;0.1 M Calcium chloride dihydrate, 20% (w/v) PEG 6000, 10% (v/v) Ethylene glycol Resolution 1.35 Å R-free 0.166

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 9yhe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9yhe
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 (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_guinier30.57
Radius of gyration Rg (electron density) rg_electron29.75
Forward intensity I(0) i096572200.00
Molecular weight molecular_weight74341.0 kDa
Excluded volume excluded_volume91809 ų
Envelope volume envelope_volume119910 ų
Hydration-shell volume shell_volume34474 ų
Envelope diameter envelope_diameter110.4
Shell Rg shell_rg36.09
Envelope Rg envelope_rg29.33
Shape Rg shape_rg29.76
Total Rg total_rg30.31
Total atoms total_atoms10305
Residues n_residues664
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 dmax101.5
Rg (real space) rg_real30.52
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real9.6570e+07
I(0) uncertainty (real space) i0_real_error1.8040e+06
Rg (reciprocal space) rg_reciprocal30.54
I(0) (reciprocal space) i0_reciprocal96570000.0000
Solution quality estimate total_estimate0.8119
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary41.0
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23870000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; 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)