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: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1016/j.immuni.2018.03.026
  • Primary Citation of Related Structures:  

  • 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 unsucce ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein H
A
697Epstein-Barr virus (strain GD1)Mutation(s): 0 
Gene Names: BXLF2 (gH)
Find proteins for K9US75 (Epstein-Barr virus (strain GD1))
Go to UniProtKB:  K9US75
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein L
B
139Epstein-Barr virus (strain AG876)Mutation(s): 0 
Gene Names: gL
Find proteins for Q1HVF6 (Epstein-Barr virus (strain AG876))
Go to UniProtKB:  Q1HVF6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Glycoprotein 42
C
227Epstein-Barr virus (strain GD1)Mutation(s): 0 
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1))
Go to UniProtKB:  P0C6Z5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab AMMO1 heavy chain
H
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab AMMO1 light chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM120553
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesHHSN272201700059C

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release