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 

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This is version 2.0 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: 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 ...

    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.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA kartik.chandran@einstein.yu.edu erica@scripps.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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))
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Go to UniProtKB:  Q05320
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence 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))
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Go to UniProtKB:  P87666
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
KZ52 Antibody FragmentO [auth A], C [auth E], G [auth I], K [auth M]226Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
KZ52 Antibody FragmentP [auth B], D [auth F], H [auth J], L [auth N]217Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseQ, R, S, T7N-Glycosylation Oligosaccharides Interaction
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

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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