5EOQ

Structure of the murine Fab 1G6 bound to the vaccinia virus A27 peptide 31-40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox.

Kaever, T.Matho, M.H.Meng, X.Crickard, L.Schlossman, A.Xiang, Y.Crotty, S.Peters, B.Zajonc, D.M.

(2016) J.Virol. 90: 4334-4345

  • DOI: 10.1128/JVI.02878-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vaccinia virus (VACV) A27 is a target for viral neutralization and part of the Dryvax smallpox vaccine. A27 is one of the three glycosaminoglycan (GAG) adhesion molecules and binds to heparan sulfate. To understand the function of anti-A27 antibodies ...

    Vaccinia virus (VACV) A27 is a target for viral neutralization and part of the Dryvax smallpox vaccine. A27 is one of the three glycosaminoglycan (GAG) adhesion molecules and binds to heparan sulfate. To understand the function of anti-A27 antibodies, especially their protective capacity and their interaction with A27, we generated and subsequently characterized 7 murine monoclonal antibodies (MAbs), which fell into 4 distinct epitope groups (groups I to IV). The MAbs in three groups (groups I, III, and IV) bound to linear peptides, while the MAbs in group II bound only to VACV lysate and recombinant A27, suggesting that they recognized a conformational and discontinuous epitope. Only group I antibodies neutralized the mature virion in a complement-dependent manner and protected against VACV challenge, while a group II MAb partially protected against VACV challenge but did not neutralize the mature virion. The epitope for group I MAbs was mapped to a region adjacent to the GAG binding site, a finding which suggests that group I MAbs could potentially interfere with the cellular adhesion of A27. We further determined the crystal structure of the neutralizing group I MAb 1G6, as well as the nonneutralizing group IV MAb 8E3, bound to the corresponding linear epitope-containing peptides. Both the light and the heavy chains of the antibodies are important in binding to their antigens. For both antibodies, the L1 loop seems to dominate the overall polar interactions with the antigen, while for MAb 8E3, the light chain generally appears to make more contacts with the antigen.


    Organizational Affiliation

    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California, USA.,Division of Cell Biology, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California, USA dzajonc@liai.org.,Department of Medicine, University of California, San Diego, School of Medicine, La Jolla, California, USA.,Division of Cell Biology, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California, USA.,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.,Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti vaccinia virus A27 antibody Fab 1G6 heavy chain
H
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti vaccinia virus A27 antibody Fab 1G6 light chain
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein A27
A
10Vaccinia virus (strain Western Reserve)Mutation(s): 0 
Find proteins for P11258 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P11258
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 99.339α = 90.00
b = 99.339β = 90.00
c = 117.564γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesHHSN272200900048C

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-04-27
    Type: Database references