9PF9 | pdb_00009pf9

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

• PDB DOI: https://doi.org/10.2210/pdb9PF9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, human gammaherpesvirus 4
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-03 Released: 2025-12-24 
• Deposition Author(s): Lang, K., Kher, G., Aldridge, N.T., Pancera, M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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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

Literature

Transgenic Mouse-Derived Human Monoclonal Antibodies Targeting EBV gp350 and gp42 Provide Basis for Therapeutic Development

Chan, 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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab ATX-350-2 light chain	A [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab ATX-350-2 heavy chain	B [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BLLF1	C [auth G]	470	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BLLF1
UniProt
Find proteins for A0A0C7T6S7 (Epstein-Barr virus (strain GD1)) Explore A0A0C7T6S7  Go to UniProtKB:  A0A0C7T6S7
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	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 = 116.675	α = 90
b = 116.675	β = 90
c = 200.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Lang, K., Kher, G., Aldridge, N.T., Pancera, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA285227

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release