6U50

Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)

  • Classification: IMMUNE SYSTEM
  • Expression System: Escherichia coli

  • Deposited: 2019-08-26 Released: 2019-11-06 
  • Deposition Author(s): Taylor, A.B., Sherwood, L.J., Hart, P.J., Hayhurst, A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID); National Institutes of Health/National Center for Research Resources (NIH/NCRR) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 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. --: --

  • DOI: 10.1016/j.jmb.2019.10.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We had previously shown that three anti-Marburgvirus nanobodies (VHH or 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 ...

    We had previously shown that three anti-Marburgvirus nanobodies (VHH or 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 ebolaviral NP C-terminus. Additionally, 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 sdAb employed CDRs they also had atypical side-on approaches with framework 2 (FR2) 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 non-overlapping epitopes - "paratope duality". One mode involved paratope gullying, while the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an inter-domain crevice. The varied routes used by sdAb to engage antigen 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

    X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229.,Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227.,X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229; Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229.,Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227. Electronic address: ahayhurst@TxBiomed.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
C
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.839α = 90.00
b = 47.839β = 90.00
c = 85.378γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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