4PB0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1371/journal.pone.0099847
  • Primary Citation of Related Structures:  
    4PB0, 4PB9

  • 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 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 Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ab53 heavy chainA [auth H]220Mus musculusMutation(s): 0 
UniProt
Find proteins for Q6PIP8 (Mus musculus)
Explore Q6PIP8 
Go to UniProtKB:  Q6PIP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PIP8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ab53 light chainB [auth L]216Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
J [auth H]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth H],
D [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth H]
F [auth H]
G [auth H]
H
I [auth H]
E [auth H],
F [auth H],
G [auth H],
H,
I [auth H],
K [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.817α = 90
b = 151.817β = 90
c = 102.766γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Refinement description