8SIC

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

Starting Model: experimental
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Literature

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

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

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cy137C02 Fab heavy chainA,
E [auth H]
222Macaca fascicularisMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cy137C02 Fab light chainB,
F [auth L]
215Macaca fascicularisMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp350C [auth E],
D [auth G]
431Human herpesvirus 4 strain B95-8Mutation(s): 0 
Gene Names: BLLF1
UniProt
Find proteins for P03200 (Epstein-Barr virus (strain B95-8))
Explore P03200 
Go to UniProtKB:  P03200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03200
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth E]
H [auth E]
I [auth E]
J [auth E]
K [auth E]
G [auth E],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
L [auth E],
N [auth E],
O [auth E],
P [auth G],
Q [auth G],
R [auth G],
S [auth G],
T [auth G],
U [auth G],
V [auth G],
W [auth G],
X [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN

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M [auth E],
Y [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.047α = 90
b = 71.377β = 90
c = 395.083γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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