5HJ3

Crystal structure of host-primed Ebola virus GP, GPcl.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies.

Bornholdt, Z.A.Ndungo, E.Fusco, M.L.Bale, S.Flyak, A.I.Crowe, J.E.Chandran, K.Saphire, E.O.

(2016) mBio 7: e02154-e02115

  • DOI: https://doi.org/10.1128/mBio.02154-15
  • Primary Citation of Related Structures:  
    5HJ3

  • PubMed Abstract: 

    The filovirus surface glycoprotein (GP) mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS) that is otherwise hidden from immune surveillance. Here, we present the crystal structure of proteolytically cleaved Ebola virus GP to a resolution of 3.3 Å. We use this structure in conjunction with functional analysis of a large panel of pseudotyped viruses bearing mutant GP proteins to map the Ebola virus GP endosomal RBS at molecular resolution. Our studies indicate that binding of GP to its endosomal receptor Niemann-Pick C1 occurs in two distinct stages: the initial electrostatic interactions are followed by specific interactions with a hydrophobic trough that is exposed on the endosomally cleaved GP1 subunit. Finally, we demonstrate that monoclonal antibodies targeting the filovirus RBS neutralize all known filovirus GPs, making this conserved pocket a promising target for the development of panfilovirus therapeutics. Ebola virus uses its glycoprotein (GP) to enter new host cells. During entry, GP must be cleaved by human enzymes in order for receptor binding to occur. Here, we provide the crystal structure of the cleaved form of Ebola virus GP. We demonstrate that cleavage exposes a site at the top of GP and that this site binds the critical domain C of the receptor, termed Niemann-Pick C1 (NPC1). We perform mutagenesis to find parts of the site essential for binding NPC1 and map distinct roles for an upper, charged crest and lower, hydrophobic trough in cleaved GP. We find that this 3-dimensional site is conserved across the filovirus family and that antibody directed against this site is able to bind cleaved GP from every filovirus tested and neutralize viruses bearing those GPs.


  • Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinA [auth C],
E [auth G],
I [auth K],
M [auth O]
179Ebola virus sp.Mutation(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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinB [auth D],
F [auth H],
J [auth L],
N [auth P]
136Ebola virus - Zaire (1995)Mutation(s): 0 
Gene Names: GP
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Explore P87666 
Go to UniProtKB:  P87666
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UniProt GroupP87666
Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
KZ52 Antibody FragmentC [auth E],
G [auth I],
K [auth M],
O [auth A]
226Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
KZ52 Antibody FragmentD [auth F],
H [auth J],
L [auth N],
P [auth B]
217Homo sapiensMutation(s): 0 
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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-(1-6)-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-glucopyranose
Q, R, S, T
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G23799GS
GlyCosmos:  G23799GS
GlyGen:  G23799GS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.103α = 90
b = 193.103β = 90
c = 350.32γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary