6EAY

Structural Basis for Broad Neutralization of Ebolaviruses by an Antibody Targeting the Glycoprotein Fusion Loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

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This is version 2.1 of the entry. See complete history


Literature

Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop.

Janus, B.M.van Dyk, N.Zhao, X.A Howell, K.Soto, C.Aman, M.J.Li, Y.Fuerst, T.R.Ofek, G.

(2018) Nat Commun 9: 3934-3934

  • DOI: https://doi.org/10.1038/s41467-018-06113-4
  • Primary Citation of Related Structures:  
    6EAY

  • PubMed Abstract: 

    The severity of the 2014-2016 ebolavirus outbreak in West Africa expedited clinical development of therapeutics and vaccines though the countermeasures on hand were largely monospecific and lacked efficacy against other ebolavirus species that previously emerged. Recent studies indicate that ebolavirus glycoprotein (GP) fusion loops are targets for cross-protective antibodies. Here we report the 3.72 Å resolution crystal structure of one such cross-protective antibody, CA45, bound to the ectodomain of Ebola virus (EBOV) GP. The CA45 epitope spans multiple faces of the fusion loop stem, across both GP1 and GP2 subunits, with ~68% of residues identical across > 99.5% of known ebolavirus isolates. Extensive antibody interactions within a pan-ebolavirus small-molecule inhibitor binding cavity on GP define this cavity as a novel site of immune vulnerability. The structure elucidates broad ebolavirus neutralization through a highly conserved epitope on GP and further enables rational design and development of broadly protective vaccines and therapeutics.


  • Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CA45 light chainA [auth L]215Macaca fascicularisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CA45 heavy chainB [auth H]237Macaca fascicularisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinC [auth A]163Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05320 
Go to UniProtKB:  Q05320
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05320
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinD [auth B]319Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05320 
Go to UniProtKB:  Q05320
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05320
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.429α = 90
b = 153.429β = 90
c = 335.862γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary