8AYU | pdb_00008ayu

Crystal structure of SUDV VP40 L117A mutant

• PDB DOI: https://doi.org/10.2210/pdb8AYU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Sudan ebolavirus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-09-03 Released: 2023-09-13 
• Deposition Author(s): Werner, A.-D., Steinchen, W., Werel, L., Kowalski, K., Essen, L.-O., Becker, S.
• Funding Organization(s): LOEWE Center DRUID

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SUDV VP40 L117A mutant

Werner, A.-D., Becker, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.56 kDa 
• Atom Count: 1,924 
• Modeled Residue Count: 239 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein VP40	A	297	Sudan ebolavirus	Mutation(s): 1  Gene Names: VP40, DF49_53412gpVP40, DH33_45403gpVP40, SEBOVgp3
UniProt
Find proteins for Q5XX06 (Sudan ebolavirus (strain Human/Uganda/Gulu/2000)) Explore Q5XX06  Go to UniProtKB:  Q5XX06

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.464	α = 90
b = 90.7	β = 95.049
c = 48.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
BIOMOL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Werner, A.-D., Steinchen, W., Werel, L., Kowalski, K., Essen, L.-O., Becker, S.

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Funding Organization	Location	Grant Number
LOEWE Center DRUID	Germany	--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-04-24
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary