3HNV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    3HNS, 3HNT, 3HNV

  • 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 that contains as a major immunomodulatory molecule the polysaccharide lipoarabinomannan (LAM) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CS-35 Fab Heavy ChainA [auth H]220Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CS-35 Fab Light ChainB [auth L]214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-arabinofuranose-(1-2)-alpha-D-arabinofuranose-(1-3)-alpha-D-arabinofuranose-(1-5)-methyl alpha-D-arabinofuranosideC [auth A]4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G88885BR
GlyCosmos:  G88885BR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.785α = 90
b = 95.111β = 102.51
c = 35.666γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary