8aov

CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with GTP

Method: ELECTRON MICROSCOPY Dmax: 177.6 Å Quality: REASONABLE

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 1–535 Chain C; UniProt 1–535 Chain E; UniProt 1–535 Chain G; UniProt 1–535 Chain I; UniProt 1–535 Chain K; UniProt 1–535 Chain M; UniProt 1–535 Chain O; UniProt 1–535 Chain Q; UniProt 1–535 Chain S; UniProt 1–535 Chain V; UniProt 1–535 Chain X; UniProt 1–535 Not recorded ZN ZINC ION × 12 GTP GUANOSINE-5'-TRIPHOSPHATE × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE;blot force zero 3 seconds, 3ul sample volume Resolution 2.48 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 1–535; UniProt 1–535 Author chain C; PDBConstruct 1–535; UniProt 1–535 Author chain E; PDBConstruct 1–535; UniProt 1–535 Author chain G; PDBConstruct 1–535; UniProt 1–535 Author chain I; PDBConstruct 1–535; UniProt 1–535 Author chain K; PDBConstruct 1–535; UniProt 1–535 Author chain M; PDBConstruct 1–535; UniProt 1–535 Author chain O; PDBConstruct 1–535; UniProt 1–535 Author chain Q; PDBConstruct 1–535; UniProt 1–535 Author chain S; PDBConstruct 1–535; UniProt 1–535 Author chain V; PDBConstruct 1–535; UniProt 1–535 Author chain X; PDBConstruct 1–535; UniProt 1–535

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 8aov

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8aov
Deposition date deposition_date2022-08-08
Structure title titleCryoEM structure of the Chikungunya virus nsP1 capping pores in complex with GTP
Keywords keywordsAlphavirus Replication complex capping pores membrane pore Methyltransferase Guanylyl transferase, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier68.28
Radius of gyration Rg (electron density) rg_electron68.00
Forward intensity I(0) i05106400000.00
Molecular weight molecular_weight599720.0 kDa
Excluded volume excluded_volume747270 ų
Envelope volume envelope_volume1127700 ų
Hydration-shell volume shell_volume129310 ų
Envelope diameter envelope_diameter189.2
Shell Rg shell_rg81.94
Envelope Rg envelope_rg64.31
Shape Rg shape_rg67.97
Total Rg total_rg68.27
Total atoms total_atoms41928
Residues n_residues5352
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 dmax177.6
Rg (real space) rg_real68.05
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real5.1060e+09
I(0) uncertainty (real space) i0_real_error9.1730e+07
Rg (reciprocal space) rg_reciprocal68.89
I(0) (reciprocal space) i0_reciprocal5114000000.0000
Solution quality estimate total_estimate0.6192
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary108.1
Skewness Skewness skewness-0.122
Kurtosis Kurtosis kurtosis-0.949
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha235300000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.981; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)