4LG2 | pdb_00004lg2

Crystal structure of Reston Ebola virus VP35 RNA binding domain bound to 12-bp dsRNA

• PDB DOI: https://doi.org/10.2210/pdb4LG2/pdb
• NAKB: 4LG2

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Reston ebolavirus - Reston (1989)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-27 Released: 2013-07-10 
• Deposition Author(s): Bale, S., Julien, J.-P., Bornholdt, Z.A., Krois, A.S., Wilson, I.A., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Ebolavirus VP35 coats the backbone of double-stranded RNA for interferon antagonism.

Bale, S., Julien, J.P., Bornholdt, Z.A., Krois, A.S., Wilson, I.A., Saphire, E.O.

(2013) J Virol 87: 10385-10388

• PubMed: 23824825 
• DOI: https://doi.org/10.1128/JVI.01452-13
• Primary Citation Related Structures: 
  4LG2


• PubMed Abstract: 
  

  Recognition of viral double-stranded RNA (dsRNA) activates interferon production and immune signaling in host cells. Crystal structures of ebolavirus VP35 show that it caps dsRNA ends to prevent sensing by pattern recognition receptors such as RIG-I. In contrast, structures of marburgvirus VP35 show that it primarily coats the dsRNA backbone. Here, we demonstrate that ebolavirus VP35 also coats the dsRNA backbone in solution, although binding to the dsRNA ends probably constitutes the initial binding event.

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Organizational Affiliation: 
• Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.51 kDa 
• Atom Count: 4,703 
• Modeled Residue Count: 530 
• Deposited Residue Count: 632 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase cofactor	A, B, C, D	146	Reston ebolavirus - Reston (1989)	Mutation(s): 0  Gene Names: VP35, REBOVgp2
UniProt
Find proteins for Q8JPY0 (Reston ebolavirus (strain Reston-89)) Explore Q8JPY0  Go to UniProtKB:  Q8JPY0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
dsRNA	E, F, G [auth J], H [auth I]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.09	α = 90
b = 72.871	β = 90
c = 175.551	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Bale, S., Julien, J.-P., Bornholdt, Z.A., Krois, A.S., Wilson, I.A., Saphire, E.O.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2013-11-27
  Changes: Database references
• Version 1.3: 2017-06-14
  Changes: Structure summary
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Refinement description