3TCQ | pdb_00003tcq

Crystal Structure of matrix protein VP40 from Ebola virus Sudan

• PDB DOI: https://doi.org/10.2210/pdb3TCQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Sudan virus - Boniface, Sudan,1976
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-09 Released: 2012-10-03 
• Deposition Author(s): Clifton, M.C., Edwards, T.E., Anderson, V., Atkins, K., Raymond, A., Saphire, E.O., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

Clifton, M.C., Bruhn, J.F., Atkins, K., Webb, T.L., Baydo, R.O., Raymond, A., Lorimer, D.D., Edwards, T.E., Myler, P.J., Saphire, E.O.

(2015) J Infect Dis 212 Suppl 2: S167-S171

• PubMed: 25957961 
• DOI: https://doi.org/10.1093/infdis/jiv090
• Primary Citation Related Structures: 
  3TCQ


• PubMed Abstract: 
  

  Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease Beryllium, Bedford, Massachusetts.
Department of Immunology and Microbial Science.
Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington.
Seattle Structural Genomics Center for Infectious Disease Seattle Biomedical Research Institute.
Department of Immunology and Microbial Science The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.51 kDa 
• Atom Count: 1,970 
• Modeled Residue Count: 239 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein VP40	A	326	Sudan virus - Boniface, Sudan,1976	Mutation(s): 0  Gene Names: VP40, SEBOVgp3
UniProt
Find proteins for B0LPL6 (Sudan ebolavirus) Explore B0LPL6  Go to UniProtKB:  B0LPL6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TCQ

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.982	α = 90
b = 90.94	β = 95.86
c = 48.684	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Clifton, M.C., Edwards, T.E., Anderson, V., Atkins, K., Raymond, A., Saphire, E.O., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2025-10-22
  Changes: Structure summary