Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.98 kDa 
• Atom Count: 7574 
• Residue Count: 987 
• Unique protein chains: 1

4LDB

Crystal Structure of Ebola Virus VP40 Dimer

• DOI: 10.2210/pdb4LDB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zaire ebolavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-24 Released: 2013-08-21 
• Deposition Author(s): Bornholdt, Z.A., Ableson, D.M., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle.

Bornholdt, Z.A., Noda, T., Abelson, D.M., Halfmann, P., Wood, M.R., Kawaoka, Y., Saphire, E.O.

(2013) Cell 154: 763-774

• PubMed: 23953110 
• DOI: 10.1016/j.cell.2013.07.015
• Primary Citation of Related Structures:  
  4LDD, 4LDI, 4LDB, 4LD8, 4LDM


• PubMed Abstract: 
  

Proteins, particularly viral proteins, can be multifunctional, but the mechanisms behind multifunctionality are not fully understood. Here, we illustrate through multiple crystal structures, biochemistry, and cellular microscopy that VP40 rearranges into different structures, each with a distinct function required for the ebolavirus life cycle. A butterfly-shaped VP40 dimer traffics to the cellular membrane. Once there, electrostatic interactions trigger rearrangement of the polypeptide into a linear hexamer. These hexamers construct a multilayered, filamentous matrix structure that is critical for budding and resembles tomograms of authentic virions. A third structure of VP40, formed by a different rearrangement, is not involved in virus assembly but instead uniquely binds RNA to regulate viral transcription inside infected cells. These results provide a functional model for ebolavirus matrix assembly and the other roles of VP40 in the virus life cycle and demonstrate how a single wild-type, unmodified polypeptide can assemble into different structures for different functions.

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Organizational Affiliation: 

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein VP40	A, B, C, D	297	Zaire ebolavirus	Mutation(s): 0  Gene Names: VP40
Find proteins for Q05128 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05128  Go to UniProtKB:  Q05128

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.005	α = 90
b = 160.005	β = 90
c = 89.745	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-24 
• Released Date: 2013-08-21 
Deposition Author(s): Bornholdt, Z.A., Ableson, D.M., Saphire, E.O.

Revision History 

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references