6BLA | pdb_00006bla

Structure of AMM01 Fab, an anti EBV gH/gL neutralizing antibody

• PDB DOI: https://doi.org/10.2210/pdb6BLA/pdb

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


• Deposited: 2017-11-09 Released: 2018-04-25 
• Deposition Author(s): Pancera, M., Weidle, C., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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: https://doi.org/10.1016/j.immuni.2018.03.026
• Primary Citation 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: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. PO Box 19024, Seattle, WA 98109, USA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. PO Box 19024, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. PO Box 19024, Seattle, WA 98109, USA. Electronic address: [e-mail].
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].

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

Macromolecule Content 

• Total Structure Weight: 49.05 kDa 
• Atom Count: 3,754 
• Modeled Residue Count: 441 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMM01 Fab Heavy chain	A [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AMM01 Fab Light chain	B [auth L]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	M [auth H]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
TRS	L [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	D [auth H], E [auth H], F [auth H], N [auth L]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H, U [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth H], G [auth H], O [auth L], P [auth L], Q [auth L], R [auth L], S [auth L], T [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	I [auth H], J [auth H], K [auth H], V [auth L], W [auth L], X [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.893	α = 90
b = 69.937	β = 90
c = 136.313	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Pancera, M., Weidle, C., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Other, Structure summary
• Version 2.0: 2024-11-06
  Changes: Data collection, Database references, Polymer sequence, Structure summary