1PZ5

Structural basis of peptide-carbohydrate mimicry in an antibody combining site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of peptide-carbohydrate mimicry in an antibody combining site.

Vyas, N.K.Vyas, M.N.Chervenak, M.C.Bundle, D.R.Pinto, B.M.Quiocho, F.A.

(2003) Proc.Natl.Acad.Sci.USA 100: 15023-15028

  • DOI: 10.1073/pnas.2431286100

  • PubMed Abstract: 
  • The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O- ...

    The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O-antigen, has been determined at 1.8-A resolution. Comparison of the structure with that of the complex with the pentasaccharide antigen [-->2)-alpha-L-Rha-(1-->2)-alpha-L-Rha-(1-->3)-alpha-L-Rha-(1-->3)-beta-D-GlcNAc-(1-->2)-alpha-L-Rha-(1-->] reveals the molecular recognition process by which a peptide mimics a carbohydrate in binding to an antibody. The binding modes of the two ligands differ considerably. Octapeptide binding complements the shape of the combining site groove much better than pentasaccharide binding. Moreover, the peptide makes a much greater number of contacts (126), which are mostly van der Waals interactions, with the Fab than the saccharide (74). An unusual feature is also the involvement of 12 water molecules in mediating hydrogen bonds between residues within the peptide or of the peptide and Fab. Despite better shape complementarity and greater number of contacts, the octapeptide binds with an affinity (KA = 2.5 x 10(5) M-1, measured by calorimetry) only approximately 2-fold tighter than the pentasaccharide. The structural results are relevant to the design of peptide mimetics with improved affinity for use as vaccines.


    Related Citations: 
    • Molecular recognition of oligosaccharide epitopes by a monoclonal Fab sepcific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.
      Vyas, N.K.,Vyas, M.N.,Chervenak, M.C.,Johnson, M.A.,Pinto, B.M.,Bundle, D.R.,Quiocho, F.A.
      (2002) Biochemistry 41: 13575
    • Preliminary crystallographic analysis of a Fab specific for the O-antigen of Shigella flexneri cell surface lipopoysaccharide with and without bound saccharides
      Vyas, M.N.,Vyas, N.K.,Meikle, P.J.,Sinnott, B.,Pinto, B.M.,Bundle, D.R.,Quiocho, F.A.
      (1993) J.Mol.Biol. 231: 133


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab (SYA/J6)
A
215Mus musculusMutation(s): 0 
Gene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab (SYA/J6)
B
220Mus musculusMutation(s): 0 
Find proteins for P01801 (Mus musculus)
Go to UniProtKB:  P01801
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Octapeptide (MDWNMHAA)
C
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.310α = 90.00
b = 69.310β = 90.00
c = 198.560γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model