8aox

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

Method: ELECTRON MICROSCOPY Dmax: 200.7 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 × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain A; UniProt 1–535 Chain BA; UniProt 1–535 Chain C; UniProt 1–535 Chain DA; UniProt 1–535 Chain E; UniProt 1–535 Chain FA; UniProt 1–535 Chain G; UniProt 1–535 Chain HA; UniProt 1–535 Chain I; UniProt 1–535 Chain JA; UniProt 1–535 Chain K; UniProt 1–535 Chain LA; UniProt 1–535 Chain M; UniProt 1–535 Chain NA; UniProt 1–535 Chain O; UniProt 1–535 Chain PA; UniProt 1–535 Chain Q; UniProt 1–535 Chain RA; UniProt 1–535 Chain S; UniProt 1–535 Chain TA; UniProt 1–535 Chain V; UniProt 1–535 Chain VA; UniProt 1–535 Chain X; UniProt 1–535 Chain Z; UniProt 1–535 Not recorded ZN ZINC ION × 24 SAM S-ADENOSYLMETHIONINE × 24 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 BA; PDBConstruct 1–535; UniProt 1–535 Author chain C; PDBConstruct 1–535; UniProt 1–535 Author chain DA; PDBConstruct 1–535; UniProt 1–535 Author chain E; PDBConstruct 1–535; UniProt 1–535 Author chain FA; PDBConstruct 1–535; UniProt 1–535 Author chain G; PDBConstruct 1–535; UniProt 1–535 Author chain HA; PDBConstruct 1–535; UniProt 1–535 Author chain I; PDBConstruct 1–535; UniProt 1–535 Author chain JA; PDBConstruct 1–535; UniProt 1–535 Author chain K; PDBConstruct 1–535; UniProt 1–535 Author chain LA; PDBConstruct 1–535; UniProt 1–535 Author chain M; PDBConstruct 1–535; UniProt 1–535 Author chain NA; PDBConstruct 1–535; UniProt 1–535 Author chain O; PDBConstruct 1–535; UniProt 1–535 Author chain PA; PDBConstruct 1–535; UniProt 1–535 Author chain Q; PDBConstruct 1–535; UniProt 1–535 Author chain RA; PDBConstruct 1–535; UniProt 1–535 Author chain S; PDBConstruct 1–535; UniProt 1–535 Author chain TA; PDBConstruct 1–535; UniProt 1–535 Author chain V; PDBConstruct 1–535; UniProt 1–535 Author chain VA; PDBConstruct 1–535; UniProt 1–535 Author chain X; PDBConstruct 1–535; UniProt 1–535 Author chain Z; 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 8aox

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8aox
Deposition date deposition_date2022-08-08
Structure title titleCryoEM structure of the Chikungunya virus nsP1 capping pores in complex with SAM
Keywords keywordsAlphavirus Replication complex Capping pores Membrane pore Methyltransferase gunayltransferase VIRAL PROTEIN, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier78.99
Radius of gyration Rg (electron density) rg_electron78.15
Forward intensity I(0) i019145800000.00
Molecular weight molecular_weight1161400.0 kDa
Excluded volume excluded_volume1446000 ų
Envelope volume envelope_volume2316200 ų
Hydration-shell volume shell_volume235130 ų
Envelope diameter envelope_diameter224.0
Shell Rg shell_rg90.81
Envelope Rg envelope_rg73.28
Shape Rg shape_rg78.13
Total Rg total_rg78.32
Total atoms total_atoms81216
Residues n_residues10368
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 dmax200.7
Rg (real space) rg_real78.29
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real1.9110e+10
I(0) uncertainty (real space) i0_real_error3.2080e+08
Rg (reciprocal space) rg_reciprocal81.03
I(0) (reciprocal space) i0_reciprocal19250000000.0000
Solution quality estimate total_estimate0.8380
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary120.4
Skewness Skewness skewness-0.206
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.1000 −1
Current regularization parameter α current_alpha0.0151
Highest regularization parameter α highest_alpha827000000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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)