6z0u

CryoEM structure of the Chikungunya virus nsP1 complex

Method: ELECTRON MICROSCOPY Dmax: 207.2 Å Quality: GOOD

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

Polyprotein P1234

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 1–472 Chain BA; UniProt 1–472 Chain C; UniProt 1–472 Chain DA; UniProt 1–472 Chain E; UniProt 1–472 Chain FA; UniProt 1–472 Chain G; UniProt 1–472 Chain HA; UniProt 1–472 Chain I; UniProt 1–472 Chain JA; UniProt 1–472 Chain K; UniProt 1–472 Chain LA; UniProt 1–472 Chain M; UniProt 1–472 Chain NA; UniProt 1–472 Chain O; UniProt 1–472 Chain PA; UniProt 1–472 Chain Q; UniProt 1–472 Chain RA; UniProt 1–472 Chain S; UniProt 1–472 Chain TA; UniProt 1–472 Chain V; UniProt 1–472 Chain VA; UniProt 1–472 Chain X; UniProt 1–472 Chain Z; UniProt 1–472 Not recorded ZN ZINC ION × 24 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE;3ul of sample was spotted onto the grid and hand blotted prior to plunge freezing. Resolution 2.90 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 1–472; UniProt 1–472 Author chain BA; PDBConstruct 1–472; UniProt 1–472 Author chain C; PDBConstruct 1–472; UniProt 1–472 Author chain DA; PDBConstruct 1–472; UniProt 1–472 Author chain E; PDBConstruct 1–472; UniProt 1–472 Author chain FA; PDBConstruct 1–472; UniProt 1–472 Author chain G; PDBConstruct 1–472; UniProt 1–472 Author chain HA; PDBConstruct 1–472; UniProt 1–472 Author chain I; PDBConstruct 1–472; UniProt 1–472 Author chain JA; PDBConstruct 1–472; UniProt 1–472 Author chain K; PDBConstruct 1–472; UniProt 1–472 Author chain LA; PDBConstruct 1–472; UniProt 1–472 Author chain M; PDBConstruct 1–472; UniProt 1–472 Author chain NA; PDBConstruct 1–472; UniProt 1–472 Author chain O; PDBConstruct 1–472; UniProt 1–472 Author chain PA; PDBConstruct 1–472; UniProt 1–472 Author chain Q; PDBConstruct 1–472; UniProt 1–472 Author chain RA; PDBConstruct 1–472; UniProt 1–472 Author chain S; PDBConstruct 1–472; UniProt 1–472 Author chain TA; PDBConstruct 1–472; UniProt 1–472 Author chain V; PDBConstruct 1–472; UniProt 1–472 Author chain VA; PDBConstruct 1–472; UniProt 1–472 Author chain X; PDBConstruct 1–472; UniProt 1–472 Author chain Z; PDBConstruct 1–472; UniProt 1–472

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 6z0u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6z0u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6z0u
Deposition date deposition_date2020-05-11
Structure title titleCryoEM structure of the Chikungunya virus nsP1 complex
Keywords keywords;Capping enzyme, monotopic membrane complex, membrane bending, membrane pore, replication complex, scaffold, Spherule formation, viral factory., VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier81.14
Radius of gyration Rg (electron density) rg_electron80.61
Forward intensity I(0) i020338600000.00
Molecular weight molecular_weight1208000.0 kDa
Excluded volume excluded_volume1507800 ų
Envelope volume envelope_volume2422000 ų
Hydration-shell volume shell_volume239470 ų
Envelope diameter envelope_diameter227.9
Shell Rg shell_rg92.44
Envelope Rg envelope_rg75.52
Shape Rg shape_rg80.60
Total Rg total_rg80.74
Total atoms total_atoms84552
Residues n_residues10896
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 dmax207.2
Rg (real space) rg_real80.41
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real2.0320e+10
I(0) uncertainty (real space) i0_real_error3.4980e+08
Rg (reciprocal space) rg_reciprocal83.37
I(0) (reciprocal space) i0_reciprocal20470000000.0000
Solution quality estimate total_estimate0.8310
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary119.9
Skewness Skewness skewness-0.197
Kurtosis Kurtosis kurtosis-0.484
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.0060
Highest regularization parameter α highest_alpha896500000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)