8SGA | pdb_00008sga

Crystal structure of 770E11, a monoclonal antibody isolated from a human Epstein-Barr virus seropositive donor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8SGA

This is version 1.4 of the entry. See complete history

Literature

Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.

Joyce, M.G.Bu, W.Chen, W.H.Gillespie, R.A.Andrews, S.F.Wheatley, A.K.Tsybovsky, Y.Jensen, J.L.Stephens, T.Prabhakaran, M.Fisher, B.E.Narpala, S.R.Bagchi, M.McDermott, A.B.Nabel, G.J.Kwong, P.D.Mascola, J.R.Cohen, J.I.Kanekiyo, M.

(2025) Immunity 58: 295

  • DOI: https://doi.org/10.1016/j.immuni.2025.01.010
  • Primary Citation Related Structures: 
    8SEF, 8SGA, 8SGG, 8SGN, 8SIC, 8SM0, 8SM1

  • PubMed Abstract: 

    Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with malignancies in humans. Viral infection of B cells is initiated by the viral glycoprotein 350 (gp350) binding to complement receptor 2 (CR2). Despite decades of effort, no vaccines or curative agents have been developed, partly due to lack of atomic-level understanding of the virus-host interface. Here, we determined the 1.7 Å structure of gp350 in complex with CR2. CR2 binding of gp350 utilized the same set of Arg residues required for recognition of its natural ligand, complement C3d. We further determined the structures of gp350 in complex with three potently neutralizing antibodies (nAbs) obtained from vaccinated macaques and EBV-infected individuals. Like the CR2 interaction, these nAbs targeted the acidic pocket within the CR2-binding site on gp350 using Arg residues. Our results illustrate two axes of molecular mimicry-gp350 versus C3d and CR2 versus EBV nAbs-offering insights for EBV vaccines and therapeutics development.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Electronic address: gjoyce@eidresearch.org.

Macromolecule Content 

  • Total Structure Weight: 46.7 kDa 
  • Atom Count: 3,561 
  • Modeled Residue Count: 429 
  • Deposited Residue Count: 438 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
770E11 Fab light chainA [auth L]212Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
770E11 Fab heavy chainB [auth H]226Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth L]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.14α = 90
b = 73.08β = 90
c = 132.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH-07-2-0067

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2025-02-12
    Changes: Database references
  • Version 1.3: 2025-02-19
    Changes: Database references
  • Version 1.4: 2025-02-26
    Changes: Database references