Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.22 kDa 
• Atom Count: 3345 
• Residue Count: 418 
• Unique protein chains: 2

6U51

Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 610-738

• DOI: 10.2210/pdb6U51/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama, Sudan virus - Boniface, Sudan,1976
• Expression System: Escherichia coli
• Mutation(s): No 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 

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

• PubMed: 31626803 
• 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. 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.

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Organizational Affiliation: 

Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA. Electronic address: http://[e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)	A, C	120	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	B, D	141	Sudan virus - Boniface, Sudan,1976	Mutation(s): 0  Gene Names: NP
Find proteins for Q9QP77 (Sudan ebolavirus (strain Boniface-76)) Explore Q9QP77  Go to UniProtKB:  Q9QP77

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.881	α = 90
b = 117.881	β = 90
c = 144.959	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MR-Rosetta	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-26 
• Released Date: 2019-11-06 
Deposition Author(s): Taylor, A.B., Sherwood, L.J., Hart, P.J., Hayhurst, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI112851
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI105568
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	C06 RR012087

Revision History 

• 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