8jce

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU

Method: ELECTRON MICROSCOPY Dmax: 202.8 Å Quality: GOOD

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

mRNA-capping enzyme nsP1

Chikungunya virus strain S27-African prototype

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 homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 1–516 Chain B; UniProt 1–516 Chain C; UniProt 1–516 Chain D; UniProt 1–516 Chain E; UniProt 1–516 Chain F; UniProt 1–516 Chain G; UniProt 1–516 Chain H; UniProt 1–516 Chain I; UniProt 1–516 Chain J; UniProt 1–516 Chain K; UniProt 1–516 Chain L; UniProt 1–516 Mutation:H37A ZN ZINC ION × 12 SAH S-ADENOSYL-L-HOMOCYSTEINE × 12 YG4 [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.41 Å

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 604 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 1–516; UniProt 1–516 Author chain B; PDBConstruct 1–516; UniProt 1–516 Author chain C; PDBConstruct 1–516; UniProt 1–516 Author chain D; PDBConstruct 1–516; UniProt 1–516 Author chain E; PDBConstruct 1–516; UniProt 1–516 Author chain F; PDBConstruct 1–516; UniProt 1–516 Author chain G; PDBConstruct 1–516; UniProt 1–516 Author chain H; PDBConstruct 1–516; UniProt 1–516 Author chain I; PDBConstruct 1–516; UniProt 1–516 Author chain J; PDBConstruct 1–516; UniProt 1–516 Author chain K; PDBConstruct 1–516; UniProt 1–516 Author chain L; PDBConstruct 1–516; UniProt 1–516

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 8jce

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8jce
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8jce
Deposition date deposition_date2023-05-11
Structure title titleCryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU
Keywords keywordsnonstructural protein, Chikungunya virus, RNA cap, replication, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier72.31
Radius of gyration Rg (electron density) rg_electron72.05
Forward intensity I(0) i05651250000.00
Molecular weight molecular_weight624210.0 kDa
Excluded volume excluded_volume774710 ų
Envelope volume envelope_volume1274300 ų
Hydration-shell volume shell_volume138980 ų
Envelope diameter envelope_diameter198.8
Shell Rg shell_rg85.95
Envelope Rg envelope_rg67.49
Shape Rg shape_rg72.04
Total Rg total_rg72.23
Total atoms total_atoms43644
Residues n_residues5436
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 dmax202.8
Rg (real space) rg_real72.04
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real5.6510e+09
I(0) uncertainty (real space) i0_real_error1.1070e+08
Rg (reciprocal space) rg_reciprocal73.01
I(0) (reciprocal space) i0_reciprocal5661000000.0000
Solution quality estimate total_estimate0.8149
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary119.8
Skewness Skewness skewness-0.134
Kurtosis Kurtosis kurtosis-0.966
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0004
Highest regularization parameter α highest_alpha256400000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)