2J1U | pdb_00002j1u

Structure of a Streptococcus pneumoniae fucose binding module in complex with the blood group A-tetrasaccharide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history. 

Literature

Blood Group Antigen Recognition by a Streptococcus Pneumoniae Virulence Factor

Boraston, A.B., Wang, D., Burke, R.D.

(2006) J Biological Chem 281: 35263

  • DOI: https://doi.org/10.1074/jbc.M607620200
  • Primary Citation Related Structures: 
    2J1R, 2J1S, 2J1T, 2J1U, 2J1V, 2J22

  • PubMed Abstract: 

    The Streptococcus pneumoniae fucose utilization operon includes a gene encoding a virulence factor that belongs to family 98 in the glycoside hydrolase classification. This protein contains a C-terminal triplet of fucose binding modules that have significant amino acid sequence identity with the Anguilla anguilla fucolectin. Functional studies of these fucose binding modules reveal binding to fucosylated oligosaccharides and suggest the importance of multivalent binding. The high resolution crystal structures of ligand bound forms of one fucose binding module uncovers the molecular basis of fucose, ABH blood group antigen, and Lewisy antigen binding. These studies are extended by fluorescence microscopy to show specific binding to mouse lung tissue. These modules define a new family of carbohydrate binding modules now classified as family 47.

    • Organizational Affiliation: 
    • Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada. boraston@uvic.ca

Macromolecule Content 

  • Total Structure Weight: 34.46 kDa 
  • Atom Count: 2,657 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 302 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FUCOLECTIN-RELATED PROTEIN
A, B
151Streptococcus pneumoniae TIGR4Mutation(s): 0 
UniProt
Find proteins for A0A0H2US34 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2US34 
Go to UniProtKB:  A0A0H2US34
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2US34
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C
4N/A
Glycosylation Resources
GlyTouCan: G19524AS
GlyCosmos: G19524AS
GlyGen: G19524AS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.649α = 90
b = 60.372β = 90
c = 99.087γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary