4ije

Crystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain R312A/K319A/R322A mutant

Method: X-RAY DIFFRACTION Dmax: 86.4 Å Quality: EXCELLENT

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

Polymerase cofactor VP35

Zaire ebolavirus

UniProt Q05127

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 218–340 Fragment:interferon inhibitory domain (UNP residues 218-340) Mutation:R312A, K319A, R322A NA SODIUM ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298.15 K;2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.228
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 218–340 Fragment:interferon inhibitory domain (UNP residues 218-340) Mutation:R312A, K319A, R322A NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298.15 K;2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.228
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 218–340 Fragment:interferon inhibitory domain (UNP residues 218-340) Mutation:R312A, K319A, R322A PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298.15 K;2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.228
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 218–340 Fragment:interferon inhibitory domain (UNP residues 218-340) Mutation:R312A, K319A, R322A NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298.15 K;2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.228

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.

25 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VP35_EBOZM
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–129; UniProt 218–340 Author chain B; PDBConstruct 7–129; UniProt 218–340 Author chain C; PDBConstruct 7–129; UniProt 218–340 Author chain D; PDBConstruct 7–129; UniProt 218–340

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 4ije

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ije
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ije
Deposition date deposition_date2012-12-21
Structure title titleCrystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain R312A/K319A/R322A mutant
Keywords keywordsIFN inhibition, polymerase cofactor, RNA binding protein, interferon antagonism, virus, 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_guinier27.18
Radius of gyration Rg (electron density) rg_electron26.02
Forward intensity I(0) i047337900.00
Molecular weight molecular_weight54245.0 kDa
Excluded volume excluded_volume68343 ų
Envelope volume envelope_volume86546 ų
Hydration-shell volume shell_volume27871 ų
Envelope diameter envelope_diameter89.9
Shell Rg shell_rg33.16
Envelope Rg envelope_rg25.85
Shape Rg shape_rg26.01
Total Rg total_rg26.86
Total atoms total_atoms3805
Residues n_residues496
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 dmax86.4
Rg (real space) rg_real27.04
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real4.7340e+07
I(0) uncertainty (real space) i0_real_error6.1550e+05
Rg (reciprocal space) rg_reciprocal27.09
I(0) (reciprocal space) i0_reciprocal47340000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.102
Kurtosis Kurtosis kurtosis-0.591
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7528000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4ijea1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.388 — Filoviridae VP35-like
Superfamily Superfamily superfamilyd.388.1 — Filoviridae VP35-like
Family Family familyd.388.1.1 — Filoviridae VP35
Domain ID domain_idd4ijea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4ijeb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.388 — Filoviridae VP35-like
Superfamily Superfamily superfamilyd.388.1 — Filoviridae VP35-like
Family Family familyd.388.1.1 — Filoviridae VP35
Domain ID domain_idd4ijeb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4ijec1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.388 — Filoviridae VP35-like
Superfamily Superfamily superfamilyd.388.1 — Filoviridae VP35-like
Family Family familyd.388.1.1 — Filoviridae VP35
Domain ID domain_idd4ijec2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4ijed1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.388 — Filoviridae VP35-like
Superfamily Superfamily superfamilyd.388.1 — Filoviridae VP35-like
Family Family familyd.388.1.1 — Filoviridae VP35
Domain ID domain_idd4ijed2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id4ijeA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily950 — Filoviridae VP35, C-terminal inhibitory domain, helical subdomain
Domain ID domain_id4ijeA02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily70 — Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain
Domain ID domain_id4ijeB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily950 — Filoviridae VP35, C-terminal inhibitory domain, helical subdomain
Domain ID domain_id4ijeB02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily70 — Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain
Domain ID domain_id4ijeC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily950 — Filoviridae VP35, C-terminal inhibitory domain, helical subdomain
Domain ID domain_id4ijeC02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily70 — Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain
Domain ID domain_id4ijeD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily950 — Filoviridae VP35, C-terminal inhibitory domain, helical subdomain
Domain ID domain_id4ijeD02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily70 — Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain

8. Citations (1)

9. Files and Curves (10)