4PB0

Structure of the Fab fragment of the anti-Francisella tularensis GroEL antibody Ab53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

B-Cell Epitopes in GroEL of Francisella tularensis.

Lu, Z.Rynkiewicz, M.J.Madico, G.Li, S.Yang, C.Y.Perkins, H.M.Sompuram, S.R.Kodela, V.Liu, T.Morris, T.Wang, D.Roche, M.I.Seaton, B.A.Sharon, J.

(2014) Plos One 9: e99847-e99847

  • DOI: 10.1371/journal.pone.0099847
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The chaperonin protein GroEL, also known as heat shock protein 60 (Hsp60), is a prominent antigen in the human and mouse antibody response to the facultative intracellular bacterium Francisella tularensis (Ft), the causative agent of tularemia. In ad ...

    The chaperonin protein GroEL, also known as heat shock protein 60 (Hsp60), is a prominent antigen in the human and mouse antibody response to the facultative intracellular bacterium Francisella tularensis (Ft), the causative agent of tularemia. In addition to its presumed cytoplasmic location, FtGroEL has been reported to be a potential component of the bacterial surface and to be released from the bacteria. In the current study, 13 IgG2a and one IgG3 mouse monoclonal antibodies (mAbs) specific for FtGroEL were classified into eleven unique groups based on shared VH-VL germline genes, and seven crossblocking profiles revealing at least three non-overlapping epitope areas in competition ELISA. In a mouse model of respiratory tularemia with the highly pathogenic Ft type A strain SchuS4, the Ab64 and N200 IgG2a mAbs, which block each other's binding to and are sensitive to the same two point mutations in FtGroEL, reduced bacterial burden indicating that they target protective GroEL B-cell epitopes. The Ab64 and N200 epitopes, as well as those of three other mAbs with different crossblocking profiles, Ab53, N3, and N30, were mapped by hydrogen/deuterium exchange-mass spectrometry (DXMS) and visualized on a homology model of FtGroEL. This model was further supported by its experimentally-validated computational docking to the X-ray crystal structures of Ab64 and Ab53 Fabs. The structural analysis and DXMS profiles of the Ab64 and N200 mAbs suggest that their protective effects may be due to induction or stabilization of a conformational change in FtGroEL.


    Organizational Affiliation

    Department of Medicine, University of California, San Diego, School of Medicine, San Diego, California, United States of America.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America; Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America.,Medical Discovery Partners, LLC, Boston, Massachusetts, United States of America.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America; Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America.,Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ab53 heavy chain
H
220Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q6PIP8 (Mus musculus)
Go to UniProtKB:  Q6PIP8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ab53 light chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
H
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 151.817α = 90.00
b = 151.817β = 90.00
c = 102.766γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-01-07
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Other, Refinement description, Source and taxonomy