8SGG

Crystal structure of Cy137D09, a monoclonal antibody isolated from macaques immunized with an Epstein-Barr virus glycoprotein 350 (gp350) nanoparticle vaccine

• PDB DOI: https://doi.org/10.2210/pdb8SGG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca fascicularis
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-04-12 Released: 2024-04-17 
• Deposition Author(s): Joyce, M.G., Jensen, J.L., Chen, W.H., Kanekiyo, M.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.246 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Crystal structure of Cy137D09, a monoclonal antibody isolated from macaques immunized with an Epstein-Barr virus glycoprotein 350 (gp350) nanoparticle vaccine

Joyce, M.G., Jensen, J.L., Chen, W.H., Kanekiyo, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.56 kDa 
• Atom Count: 7,104 
• Modelled Residue Count: 892 
• Deposited Residue Count: 904 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy137D09 Fab heavy chain	A, C	232	Macaca fascicularis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy137D09 Fab light chain	B, D	220	Macaca fascicularis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth C], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.246 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.794	α = 90
b = 71.463	β = 107.25
c = 86.451	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Joyce, M.G., Jensen, J.L., Chen, W.H., Kanekiyo, M.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-07-2-0067

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release