5UK4

VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication.

Hanke, L.Schmidt, F.I.Knockenhauer, K.E.Morin, B.Whelan, S.P.Schwartz, T.U.Ploegh, H.L.

(2017) EMBO Rep. 18: 1027-1037

  • DOI: 10.15252/embr.201643764
  • Primary Citation of Related Structures:  5UKB

  • PubMed Abstract: 
  • The transcription and replication machinery of negative-stranded RNA viruses presents a possible target for interference in the viral life cycle. We demonstrate the validity of this concept through the use of cytosolically expressed single-domain ant ...

    The transcription and replication machinery of negative-stranded RNA viruses presents a possible target for interference in the viral life cycle. We demonstrate the validity of this concept through the use of cytosolically expressed single-domain antibody fragments (VHHs) that protect cells from a lytic infection with vesicular stomatitis virus (VSV) by targeting the viral nucleoprotein N. We define the binding sites for two such VHHs, 1004 and 1307, by X-ray crystallography to better understand their inhibitory properties. We found that VHH 1307 competes with the polymerase cofactor P for binding and thus inhibits replication and mRNA transcription, while binding of VHH 1004 likely only affects genome replication. The functional relevance of these epitopes is confirmed by the isolation of escape mutants able to replicate in the presence of the inhibitory VHHs. The escape mutations allow identification of the binding site of a third VHH that presumably competes with P for binding at another site than 1307. Collectively, these binding sites uncover different features on the N protein surface that may be suitable for antiviral intervention.


    Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
P, B, Q, C, R, D, S, E, T, K, L, N, M, F, G, H, I, O, J, A
422Vesicular stomatitis Indiana virus (strain San Juan)Gene Names: N
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan))
Go to UniProtKB:  P03521
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-vesicular stomatitis virus N VHH
p, b, q, c, r, d, s, e, t, k, l, n, m, f, g, h, i, o, j, a
139Vicugna pacosN/A
Find proteins for A0A192B6J6 (Vicugna pacos)
Go to UniProtKB:  A0A192B6J6
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (45-MER)u,v,w,x45Vicugna pacos
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.236 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/448 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 147.555α = 79.24
b = 156.008β = 75.66
c = 217.450γ = 62.27
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence