Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - ABCDE Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer -A2BCD 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 167604.91 
• Atom Count: 10649 
• Residue Count: 1505 
• Unique protein chains: 5

6C5V

An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus

• DOI: 10.2210/pdb6C5V/pdb
• EMDataBank: EMD-7344

• Classification: VIRAL PROTEIN
• Organism(s): Epstein-Barr virus (strain AG876), Epstein-Barr virus (strain GD1)
• Expression System: Homo sapiens


• Deposited: 2018-01-16 Released: 2018-05-02 
• Deposition Author(s): Snijder, J., Ortego, M.S., Weidle, C., Stuart, A.B., Gray, M.A., McElrath, M.J., Pancera, M., Veesler, D., McGuire, A.T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus.

Snijder, J., Ortego, M.S., Weidle, C., Stuart, A.B., Gray, M.D., McElrath, M.J., Pancera, M., Veesler, D., McGuire, A.T.

(2018) Immunity 48: 799-811.e9

• PubMed: 29669253 
• DOI: 10.1016/j.immuni.2018.03.026
• Primary Citation of Related Structures:  
  6BLA


• PubMed Abstract: 
  

Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have focused on the gp350 glycoprotein and remain unsuccessful. We isolated human antibodies recognizing the EBV fusion machinery (gH/gL and gB) from rare memory B cells. One anti-gH/gL antibody, AMMO1, potently neutralized infection of B cells and epithelial cells, the two major cell types targeted by EBV. We determined a cryo-electron microscopy reconstruction of the gH/gL-gp42-AMMO1 complex and demonstrated that AMMO1 bound to a discontinuous epitope formed by both gH and gL at the Domain-I/Domain-II interface. Integrating structural, biochemical, and infectivity data, we propose that AMMO1 inhibits fusion of the viral and cellular membranes. This work identifies a crucial epitope that may aid in the design of next-generation subunit vaccines against this major public health burden.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein H	A	697	Epstein-Barr virus (strain GD1)	Mutation(s): 0  Gene Names: BXLF2 (gH)
Find proteins for K9US75 (Epstein-Barr virus (strain GD1)) Go to UniProtKB:  K9US75

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein L	B	139	Epstein-Barr virus (strain AG876)	Mutation(s): 0  Gene Names: gL
Find proteins for Q1HVF6 (Epstein-Barr virus (strain AG876)) Go to UniProtKB:  Q1HVF6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Glycoprotein 42	C	227	Epstein-Barr virus (strain GD1)	Mutation(s): 0
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1)) Go to UniProtKB:  P0C6Z5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Antibody Fab AMMO1 heavy chain	H	226	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Antibody Fab AMMO1 light chain	L	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	H	L-PEPTIDE LINKING	C5 H7 N O3		GLU

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-16 
• Released Date: 2018-05-02 
• Deposition Author(s): Snijder, J., Ortego, M.S., Weidle, C., Stuart, A.B., Gray, M.A., McElrath, M.J., Pancera, M., Veesler, D., McGuire, A.T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	R01GM120553
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	HHSN272201700059C

Revision History 

• Version 1.0: 2018-05-02
  Type: Initial release