3gpg

Crystal structure of macro domain of Chikungunya virus

Method: X-RAY DIFFRACTION Dmax: 94.9 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:sequence database residues 1334-1493 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;46% PEG 600, 100 mM hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.196
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1334–1493 Fragment:sequence database residues 1334-1493 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;46% PEG 600, 100 mM hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.196
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1334–1493 Fragment:sequence database residues 1334-1493 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;46% PEG 600, 100 mM hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.196
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1334–1493 Fragment:sequence database residues 1334-1493 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;46% PEG 600, 100 mM hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.196

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 3gpg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gpg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gpg
Deposition date deposition_date2009-03-23
Structure title titleCrystal structure of macro domain of Chikungunya virus
Keywords keywords;macro domain, X domain, Chikungunya, alphavirus, virus, VIZIER. Viral enzymes involved in replication, ATP-binding, Cell membrane, Endosome, Helicase, Hydrolase, Lipoprotein, Lysosome, Membrane, Methyltransferase, mRNA capping, mRNA processing, Multifunctional enzyme, Nucleotide-binding, Nucleotidyltransferase, Nucleus, Palmitate, Phosphoprotein, Protease, RNA replication, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.86
Radius of gyration Rg (electron density) rg_electron29.01
Forward intensity I(0) i084418000.00
Molecular weight molecular_weight70092.0 kDa
Excluded volume excluded_volume86883 ų
Envelope volume envelope_volume110830 ų
Hydration-shell volume shell_volume32209 ų
Envelope diameter envelope_diameter99.7
Shell Rg shell_rg35.83
Envelope Rg envelope_rg28.65
Shape Rg shape_rg29.00
Total Rg total_rg29.69
Total atoms total_atoms4915
Residues n_residues643
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 dmax94.9
Rg (real space) rg_real29.80
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real8.4420e+07
I(0) uncertainty (real space) i0_real_error1.1370e+06
Rg (reciprocal space) rg_reciprocal29.83
I(0) (reciprocal space) i0_reciprocal84420000.0000
Solution quality estimate total_estimate0.9028
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.2
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.566
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28530000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.944

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3gpgA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3gpgB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3gpgC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3gpgD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1

8. Citations (1)

9. Files and Curves (10)