6C5V

An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus.

Snijder, J.Ortego, M.S.Weidle, C.Stuart, A.B.Gray, M.D.McElrath, M.J.Pancera, M.Veesler, D.McGuire, A.T.

(2018) Immunity 48: 799-811.e9

  • DOI: https://doi.org/10.1016/j.immuni.2018.03.026
  • Primary Citation of Related Structures:  
    6BLA, 6C5V

  • PubMed Abstract: 

    Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have focused on the gp350 glycoprotein and remain unsuccessful. We isolated human antibodies recognizing the EBV fusion machinery (gH/gL and gB) from rare memory B cells. One anti-gH/gL antibody, AMMO1, potently neutralized infection of B cells and epithelial cells, the two major cell types targeted by EBV. We determined a cryo-electron microscopy reconstruction of the gH/gL-gp42-AMMO1 complex and demonstrated that AMMO1 bound to a discontinuous epitope formed by both gH and gL at the Domain-I/Domain-II interface. Integrating structural, biochemical, and infectivity data, we propose that AMMO1 inhibits fusion of the viral and cellular membranes. This work identifies a crucial epitope that may aid in the design of next-generation subunit vaccines against this major public health burden.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein H697human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BXLF2gH
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein L139Epstein-barr virus strain ag876Mutation(s): 0 
Gene Names: gLBKRF2
UniProt
Find proteins for Q1HVF6 (Epstein-Barr virus (strain AG876))
Explore Q1HVF6 
Go to UniProtKB:  Q1HVF6
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1HVF6
Glycosylation
Glycosylation Sites: 2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein 42227human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BZLF2
UniProt
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1))
Explore P0C6Z5 
Go to UniProtKB:  P0C6Z5
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6Z5
Glycosylation
Glycosylation Sites: 3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab AMMO1 heavy chainD [auth H]226Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab AMMO1 light chainE [auth L]216Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseF [auth D]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
D [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 2.0: 2019-12-18
    Changes: Author supporting evidence, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary