6EAY | pdb_00006eay

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 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.260 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6EAY

Ligand Structure Quality Assessment 


This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 104.26 kDa 
  • Atom Count: 5,376 
  • Modeled Residue Count: 747 
  • Deposited Residue Count: 934 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CA45 light chainA [auth L]215Macaca fascicularisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CA45 heavy chainB [auth H]237Macaca fascicularisMutation(s): 0 
Find similar proteins by:|  3D Structure
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
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free:  0.297 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.260 (Depositor) 
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

View Full Validation Report



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
  • Version 2.2: 2024-10-16
    Changes: Structure summary