4YPI

Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.8 of the entry. See complete history


Literature

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.

Leung, D.W.Borek, D.Luthra, P.Binning, J.M.Anantpadma, M.Liu, G.Harvey, I.B.Su, Z.Endlich-Frazier, A.Pan, J.Shabman, R.S.Chiu, W.Davey, R.A.Otwinowski, Z.Basler, C.F.Amarasinghe, G.K.

(2015) Cell Rep 11: 376-389

  • DOI: 10.1016/j.celrep.2015.03.034
  • Primary Citation of Related Structures:  
    4YPI

  • PubMed Abstract: 
  • During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented f ...

    During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA. Electronic address: gamarasinghe@path.wustl.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinABCD348Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: NP
Find proteins for P18272 (Zaire ebolavirus (strain Mayinga-76))
Explore P18272 
Go to UniProtKB:  P18272
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase cofactor VP35EFGH28Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05127 
Go to UniProtKB:  Q05127
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.752α = 90
b = 194.818β = 90
c = 347.684γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000phasing
SHELXDEphasing
HKL-3000data reduction

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 StatesR01AI081914
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI109945
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI109664
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI109664
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50GM1003297
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI059536
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI077519
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI107056
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM053163
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103399
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
Defense Threat Reduction Agency (DTRA)United StatesDTRA 1_21_1_0002
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1_12_1_0051
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1_14_1_0013

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-05-06
    Changes: Database references
  • Version 1.3: 2016-08-24
    Changes: Other
  • Version 1.4: 2016-08-31
    Changes: Other, Structure summary
  • Version 1.5: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.6: 2017-11-22
    Changes: Refinement description
  • Version 1.7: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.8: 2019-12-04
    Changes: Author supporting evidence