3gpo

Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose

Method: X-RAY DIFFRACTION Dmax: 96.0 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 Non-standard monomer:Yes (specific site not provided by mmCIF) APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 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 1.90 Å R-free 0.201
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 Non-standard monomer:Yes (specific site not provided by mmCIF) APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 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 1.90 Å R-free 0.201
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 Non-standard monomer:Yes (specific site not provided by mmCIF) APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 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 1.90 Å R-free 0.201
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 Non-standard monomer:Yes (specific site not provided by mmCIF) APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 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 1.90 Å R-free 0.201

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 3gpo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3gpo
Deposition date deposition_date2009-03-23
Structure title titleCrystal structure of macro domain of Chikungunya virus in complex with ADP-ribose
Keywords keywords;macro domain, X domain, Chikungunya, alphavirus, virus, VIZIER. Viral enzymes involved in replication, ADP-ribose, 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_guinier30.10
Radius of gyration Rg (electron density) rg_electron29.35
Forward intensity I(0) i097865200.00
Molecular weight molecular_weight73134.0 kDa
Excluded volume excluded_volume89318 ų
Envelope volume envelope_volume113710 ų
Hydration-shell volume shell_volume32866 ų
Envelope diameter envelope_diameter100.0
Shell Rg shell_rg36.00
Envelope Rg envelope_rg28.99
Shape Rg shape_rg29.35
Total Rg total_rg29.96
Total atoms total_atoms5060
Residues n_residues623
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 dmax96.0
Rg (real space) rg_real30.02
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real9.7870e+07
I(0) uncertainty (real space) i0_real_error1.4230e+06
Rg (reciprocal space) rg_reciprocal30.06
I(0) (reciprocal space) i0_reciprocal97870000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.5
Skewness Skewness skewness0.158
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44560000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3gpoA00
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_id3gpoB00
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_id3gpoC00
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_id3gpoD00
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)