6E5X

Crystal structure of Ebola virus VP30 C-terminus/RBBP6 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.

Batra, J.Hultquist, J.F.Liu, D.Shtanko, O.Von Dollen, J.Satkamp, L.Jang, G.M.Luthra, P.Schwarz, T.M.Small, G.I.Arnett, E.Anantpadma, M.Reyes, A.Leung, D.W.Kaake, R.Haas, P.Schmidt, C.B.Schlesinger, L.S.LaCount, D.J.Davey, R.A.Amarasinghe, G.K.Basler, C.F.Krogan, N.J.

(2018) Cell 175: 1917-1930.e13

  • DOI: 10.1016/j.cell.2018.08.044
  • Primary Citation of Related Structures:  
    6E5X

  • PubMed Abstract: 
  • Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host pro ...

    Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host protein-protein interaction (PPI) map. We uncovered 194 high-confidence EBOV-human PPIs, including one between the viral transcription regulator VP30 and the host ubiquitin ligase RBBP6. Domain mapping identified a 23 amino acid region within RBBP6 that binds to VP30. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30. Knockdown of endogenous RBBP6 stimulated viral transcription and increased EBOV replication, whereas overexpression of either RBBP6 or the peptide strongly inhibited both. These results demonstrate the therapeutic potential of biologics that target this interface and identify additional PPIs that may be leveraged for novel therapeutic strategies.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA. Electronic address: nevan.krogan@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Minor nucleoprotein VP30A127Ebola virus - Zaire (1995)Mutation(s): 0 
Gene Names: VP30
Find proteins for Q77DJ5 (Zaire ebolavirus (strain Kikwit-95))
Explore Q77DJ5 
Go to UniProtKB:  Q77DJ5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBBP6B15Homo sapiensMutation(s): 0 
Gene Names: RBBP6P2PRPACTRBQ1My038
EC: 2.3.2.27
Find proteins for Q7Z6E9 (Homo sapiens)
Explore Q7Z6E9 
Go to UniProtKB:  Q7Z6E9
NIH Common Fund Data Resources
PHAROS  Q7Z6E9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.6α = 90
b = 45.6β = 90
c = 158.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI120943
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI123926

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence