9PF9 | pdb_00009pf9

X-ray crystal structure of ATX-350-2 Fab bound to Epstein-Barr virus glycoprotein 350


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 
    0.282 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Models: experimental, in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Transgenic mouse-derived human monoclonal antibodies targeting EBV gp350 and gp42 provide basis for therapeutic development.

Chhan, C.B.Lang, K.Davis, A.R.Wan, Y.H.Aldridge, N.T.Kher, G.Scharffenberger, S.C.Hardy, S.R.Iureniev, R.Giltiay, N.V.Edwards, K.R.Radtke, S.Kiem, H.P.Pancera, M.McGuire, A.T.

(2026) Cell Rep Med 7: 102618-102618

  • DOI: https://doi.org/10.1016/j.xcrm.2026.102618
  • Primary Citation Related Structures: 
    9PF9

  • PubMed Abstract: 

    Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk of post-transplant lymphoproliferative disease, a life-threatening EBV-driven lymphoma. There are no EBV-specific vaccines or treatments; however, neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents. EBV entry into B cells involves gp350, which binds complement receptors, and gp42, which engages HLA class II to trigger fusion. Most existing monoclonal antibodies (mAbs) against these antigens are non-human, limiting clinical use. Using a transgenic mouse model, we generate two gp350 and eight gp42 genetically human neutralizing mAbs that block receptor binding. Structural analyses reveal extended sites of vulnerability relevant to vaccine development. Delivery of a gp42 mAb protects humanized mice from EBV challenge, while a gp350 mAb provides partial protection. These mAbs highlight the utility of transgenic mice to produce therapeutic mAbs for preventing EBV-driven disease.


  • Organizational Affiliation
    • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98105, USA.

Macromolecule Content 

  • Total Structure Weight: 98.47 kDa 
  • Atom Count: 6,503 
  • Modeled Residue Count: 843 
  • Deposited Residue Count: 904 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab ATX-350-2 light chainA [auth L]214Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab ATX-350-2 heavy chainB [auth H]220Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
BLLF1C [auth G]470human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BLLF1
UniProt
Find proteins for A0A0C7T6S7 (Epstein-Barr virus (strain GD1))
Explore A0A0C7T6S7 
Go to UniProtKB:  A0A0C7T6S7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C7T6S7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
E [auth G]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free:  0.282 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.675α = 90
b = 116.675β = 90
c = 200.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA285227

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Database references