5UK4

VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.15252/embr.201643764
  • Primary Citation of Related Structures:  
    5UK4, 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 antibody fragments (VHHs) that protect cells from a lytic infection with vesicular stomatitis virus (VSV) by targeting the viral nucleoprotein N ...

    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: 

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein422Vesicular stomatitis Indiana virus strain San JuanMutation(s): 0 
Gene Names: N
UniProt
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan))
Explore P03521 
Go to UniProtKB:  P03521
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03521
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-vesicular stomatitis virus N VHH139Vicugna pacosMutation(s): 0 
UniProt
Find proteins for A0A192B6J6 (Vicugna pacos)
Explore A0A192B6J6 
Go to UniProtKB:  A0A192B6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A192B6J6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (45-MER)OA [auth u],
PA [auth v],
QA [auth w],
RA [auth x]		45Vicugna pacos
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.555α = 79.24
b = 156.008β = 75.66
c = 217.45γ = 62.27
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2020-02-26
    Changes: Data collection