Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167.51 kDa 
• Atom Count: 10649 
• Residue Count: 1353 
• 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
• EMDataResource: EMD-7344

• Classification: VIRAL PROTEIN
• Organism(s): Human gammaherpesvirus 4, Homo sapiens, Epstein-barr virus strain ag876
• Expression System: Homo sapiens
• Mutation(s): No 


• 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 (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 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, 6C5V


• 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: 

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. PO Box 19024, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A	697	Human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BXLF2, gH
Find proteins for K9US75 (Epstein-Barr virus (strain GD1)) Explore K9US75  Go to UniProtKB:  K9US75

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 42	C	227	Human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BZLF2
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1)) Explore P0C6Z5  Go to UniProtKB:  P0C6Z5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab AMMO1 heavy chain	H	226	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab AMMO1 light chain	L	216	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B	139	Epstein-barr virus strain ag876	Mutation(s): 0  Gene Names: gL, BKRF2
Find proteins for Q1HVF6 (Epstein-Barr virus (strain AG876)) Explore Q1HVF6  Go to UniProtKB:  Q1HVF6

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose 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		GLN

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 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 (NIH/NIGMS)	United States	R01GM120553
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History 

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 2.0: 2019-12-18
  Changes: Author supporting evidence, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary