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 

wwPDB Validation 3D Report Full Report


This is version 1.7 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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
C, A, B, D
348Zaire ebolavirus (strain Mayinga-76)Gene Names: NP
Find proteins for P18272 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  P18272
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polymerase cofactor VP35
G, E, F, H
28Zaire ebolavirus (strain Mayinga-76)Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05127
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.752α = 90.00
b = 194.818β = 90.00
c = 347.684γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-2000data collection
HKL-3000phasing
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
SHELXDEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI081914
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU19AI109945
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU19AI109664
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU19AI109664
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesHHSN272201200026C
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103832
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50GM1003297
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI059536
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI077519
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI107056
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM053163
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103399
Department of Energy (United States)United StatesDE-AC02-06CH11357
Defense Threat Reduction AgencyUnited StatesDTRA 1_21_1_0002
Defense Threat Reduction AgencyUnited StatesHDTRA1_12_1_0051
Defense Threat Reduction AgencyUnited StatesHDTRA1_14_1_0013

Revision History 

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