3HNV

CS-35 Fab Complex with Oligoarabinofuranosyl Tetrasaccharide (branch part of Hexasaccharide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into antibody recognition of mycobacterial polysaccharides.

Murase, T.Zheng, R.B.Joe, M.Bai, Y.Marcus, S.L.Lowary, T.L.Ng, K.K.

(2009) J.Mol.Biol. 392: 381-392

  • DOI: 10.1016/j.jmb.2009.06.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacteria are major human pathogens responsible for such serious and widespread diseases as tuberculosis and leprosy. Among the evolutionary adaptations essential for pathogenicity in mycobacteria is a complex carbohydrate-rich cell-wall structure ...

    Mycobacteria are major human pathogens responsible for such serious and widespread diseases as tuberculosis and leprosy. Among the evolutionary adaptations essential for pathogenicity in mycobacteria is a complex carbohydrate-rich cell-wall structure that contains as a major immunomodulatory molecule the polysaccharide lipoarabinomannan (LAM). We report here crystal structures of three fragments from the non-reducing termini of LAM in complex with a murine antibody Fab fragment (CS-35Fab). These structures reveal for the first time the three-dimensional structures of key components of LAM and the molecular basis of LAM recognition at between 1.8- and 2.0-A resolution. The antigen-binding site of CS-35Fab forms three binding pockets that show a high degree of complementarity to the reducing end, the branch point and one of the non-reducing ends of the Y-shaped hexasaccharide moiety found at most of the non-reducing termini of LAM. Structures of CS-35Fab bound to two additional tetrasaccharides confirm the general mode of binding seen in the hexasaccharide and indicate how different parts of LAM are recognized. Altogether, these structures provide a rational basis for understanding the overall architecture of LAM and identify the key elements of an epitope that may be exploited for the development of novel and more effective anti-mycobacterial vaccines. Moreover, this study represents the first high-resolution X-ray crystallographic investigation of oligofuranoside-protein recognition.


    Organizational Affiliation

    Alberta Ingenuity Centre for Carbohydrate Science, University of Calgary, Calgary, Alberta, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CS-35 Fab Heavy Chain
H
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CS-35 Fab Light Chain
L
214N/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
BXX
Query on BXX

Download SDF File 
Download CCD File 
H
beta-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-SQOUGZDYSA-N
 Ligand Interaction
BXY
Query on BXY

Download SDF File 
Download CCD File 
H
alpha-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-MBMOQRBOSA-N
 Ligand Interaction
AXR
Query on AXR

Download SDF File 
Download CCD File 
H
methyl alpha-D-arabinofuranoside
1-O-methyl-alpha-D-arabinofuranoside
C6 H12 O5
NALRCAPFICWVAQ-ZXXMMSQZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.785α = 90.00
b = 95.111β = 102.51
c = 35.666γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
REFMACrefinement
Blu-Icedata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance