3HNS | pdb_00003hns

CS-35 Fab Complex with Oligoarabinofuranosyl Hexasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.217 (Depositor) 
  • R-Value Work: 
    0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3HNS

This is version 2.2 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 Biology 392: 381-392

  • DOI: https://doi.org/10.1016/j.jmb.2009.06.074
  • Primary Citation 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). 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.

Macromolecule Content 

  • Total Structure Weight: 48.35 kDa 
  • Atom Count: 3,904 
  • Modeled Residue Count: 434 
  • Deposited Residue Count: 434 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CS-35 Fab Heavy ChainA [auth H]220Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CS-35 Fab Light ChainB [auth L]214Mus musculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-arabinofuranose-(1-2)-alpha-D-arabinofuranose-(1-3)-[beta-D-arabinofuranose-(1-2)-alpha-D-arabinofuranose-(1-5)]alpha-D-arabinofuranose-(1-5)-methyl alpha-D-arabinofuranosideC [auth A]6N/A
Glycosylation Resources
GlyTouCan: G59963AK
GlyCosmos: G59963AK

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.217 (Depositor) 
  • R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.725α = 90
b = 96.234β = 102.35
c = 36.065γ = 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
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-27
    Changes: Structure summary