4LU5 | pdb_00004lu5

Structure of murine IgG2a A20G2-Fab in complex with vaccinia antigen A33R at the resolution of 2.9 Angstroms

• PDB DOI: https://doi.org/10.2210/pdb4LU5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Orthopoxvirus vaccinia, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Mus musculus
• Mutation(s): Yes 


• Deposited: 2013-07-24 Released: 2014-07-30 
• Deposition Author(s): Matho, M.H., Schlossman, A.M., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.282 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer.

Matho, M.H., Schlossman, A., Meng, X., Benhnia, M.R., Kaever, T., Buller, M., Doronin, K., Parker, S., Peters, B., Crotty, S., Xiang, Y., Zajonc, D.M.

(2015) PLoS Pathog 11: e1005148-e1005148

• PubMed: 26325270 
• DOI: https://doi.org/10.1371/journal.ppat.1005148
• Primary Citation Related Structures: 
  4LQF, 4LU5, 4M1G


• PubMed Abstract: 
  

  Vaccinia virus A33 is an extracellular enveloped virus (EEV)-specific type II membrane glycoprotein that is essential for efficient EEV formation and long-range viral spread within the host. A33 is a target for neutralizing antibody responses against EEV. In this study, we produced seven murine anti-A33 monoclonal antibodies (MAbs) by immunizing mice with live VACV, followed by boosting with the soluble A33 homodimeric ectodomain. Five A33 specific MAbs were capable of neutralizing EEV in the presence of complement. All MAbs bind to conformational epitopes on A33 but not to linear peptides. To identify the epitopes, we have adetermined the crystal structures of three representative neutralizing MAbs in complex with A33. We have further determined the binding kinetics for each of the three antibodies to wild-type A33, as well as to engineered A33 that contained single alanine substitutions within the epitopes of the three crystallized antibodies. While the Fab of both MAbs A2C7 and A20G2 binds to a single A33 subunit, the Fab from MAb A27D7 binds to both A33 subunits simultaneously. A27D7 binding is resistant to single alanine substitutions within the A33 epitope. A27D7 also demonstrated high-affinity binding with recombinant A33 protein that mimics other orthopoxvirus strains in the A27D7 epitope, such as ectromelia, monkeypox, and cowpox virus, suggesting that A27D7 is a potent cross-neutralizer. Finally, we confirmed that A27D7 protects mice against a lethal challenge with ectromelia virus.

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Organizational Affiliation: 
• Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
Department of Microbiology and Immunology, University of Texas Health Science Center, San Antonio, Texas, United States of America.
Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville; and Laboratory of Immunovirology, Unit 211, Biomedicine Institute of Seville (IBIS), Seville, Spain.
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
Saint Louis University School of Medicine, St. Louis, Missouri, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.7 kDa 
• Atom Count: 8,008 
• Modeled Residue Count: 1,030 
• Deposited Residue Count: 1,058 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A33R	A, B	97	Orthopoxvirus vaccinia	Mutation(s): 4
UniProt
Find proteins for Q71TT1 (Vaccinia virus) Explore Q71TT1  Go to UniProtKB:  Q71TT1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Murine IgG2a A20G2 Heavy chain Fab domain	C [auth H], D [auth I]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Murine IgG2a A20G2 Light chain Fab domain	E [auth L], F [auth M]	219	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.282 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.9	α = 90
b = 157.261	β = 90
c = 175.89	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Matho, M.H., Schlossman, A.M., Zajonc, D.M.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary