6Z0O

Structure of Affimer-NP bound to Crimean-Congo Haemorrhagic Fever Virus Nucleocapsid Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization and applications of a Crimean-Congo hemorrhagic fever virus nucleoprotein-specific Affimer: Inhibitory effects in viral replication and development of colorimetric diagnostic tests.

Alvarez-Rodriguez, B.Tiede, C.Hoste, A.C.R.Surtees, R.A.Trinh, C.H.Slack, G.S.Chamberlain, J.Hewson, R.Fresco, A.Sastre, P.Tomlinson, D.C.Millner, P.A.Edwards, T.A.Barr, J.N.

(2020) PLoS Negl Trop Dis 14: e0008364-e0008364

  • DOI: https://doi.org/10.1371/journal.pntd.0008364
  • Primary Citation of Related Structures:  
    6Z0O

  • PubMed Abstract: 

    Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) is one of the most widespread medically important arboviruses, causing human infections that result in mortality rates of up to 60%. We describe the selection of a high-affinity small protein (Affimer-NP) that binds specifically to the nucleoprotein (NP) of CCHFV. We demonstrate the interference of Affimer-NP in the RNA-binding function of CCHFV NP using fluorescence anisotropy, and its inhibitory effects on CCHFV gene expression in mammalian cells using a mini-genome system. Solution of the crystallographic structure of the complex formed by these two molecules at 2.84 Å resolution revealed the structural basis for this interference, with the Affimer-NP binding site positioned at the critical NP oligomerization interface. Finally, we validate the in vitro application of Affimer-NP for the development of enzyme-linked immunosorbent and lateral flow assays, presenting the first published point-of-care format test able to detect recombinant CCHFV NP in spiked human and animal sera.


  • Organizational Affiliation

    School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleocapsid
A, B
482Orthonairovirus haemorrhagiaeMutation(s): 0 
Gene Names: Np
UniProt
Find proteins for Q70UR4 (Orthonairovirus haemorrhagiae)
Explore Q70UR4 
Go to UniProtKB:  Q70UR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70UR4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Affimer-NPC [auth E],
D [auth F]
90synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.33α = 90
b = 73.98β = 100.923
c = 95.764γ = 90
Software Package:
Software NamePurpose
xia2data processing
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)United Kingdom721367

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description