6U55

Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 634-738


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins.

Sherwood, L.J.Taylor, A.B.Hart, P.J.Hayhurst, A.

(2019) J Mol Biol 431: 4848-4867

  • DOI: 10.1016/j.jmb.2019.10.005
  • Primary Citation of Related Structures:  
    6U51, 6U50, 6U53, 6U52, 6U55, 6U54

  • PubMed Abstract: 
  • We had previously shown that three anti-Marburg virus nanobodies (VHH or single-domain antibody [sdAb]) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution ...

    We had previously shown that three anti-Marburg virus nanobodies (VHH or single-domain antibody [sdAb]) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti-Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolavirus NP C-terminus. In addition, we sought to determine whether the specificities of a less cross-reactive anti-Zaire ebolavirus sdAb and a totally specific anti-Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus-specific sdAb, arose from the footprint shifting away from the helices to engage more variable residues. While both sdAbs used CDRs, they also had atypical side-on approaches, with framework 2 helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus-specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via nonoverlapping epitopes-"paratope duality." One mode involved paratope gullying, whereas the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an interdomain crevice. The varied routes used by sdAbs to engage antigens discovered here deepen our appreciation of the small scaffold's architectural versatility and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting.


    Organizational Affiliation

    Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA. Electronic address: http://ahayhurst@TxBiomed.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE) A117Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein B117Sudan virus - Boniface, Sudan,1976Mutation(s): 0 
Gene Names: NP
Find proteins for Q9QP77 (Sudan ebolavirus (strain Boniface-76))
Explore Q9QP77 
Go to UniProtKB:  Q9QP77
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.398α = 90
b = 28.298β = 114.453
c = 86.541γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

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 StatesR01 AI112851
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI105568
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesC06 RR012087

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-11
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Database references