Structure of the Corynebacterium diphtheriae major pilin SpaA points to a modular pilus assembly with stabilizing isopeptide bonds

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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The Corynebacterium diphtheriae shaft pilin SpaA is built of tandem Ig-like modules with stabilizing isopeptide and disulfide bonds

Kang, H.J.Paterson, N.G.Gaspar, A.H.Ton-That, H.Baker, E.N.

(2009) Proc Natl Acad Sci U S A 106: 16967-16971

  • DOI: https://doi.org/10.1073/pnas.0906826106
  • Primary Citation of Related Structures:  
    3HR6, 3HTL

  • PubMed Abstract: 

    Cell-surface pili are important virulence factors that enable bacterial pathogens to adhere to specific host tissues and modulate host immune response. Relatively little is known about the structure of Gram-positive bacterial pili, which are built by the sortase-catalyzed covalent crosslinking of individual pilin proteins. Here we report the 1.6-A resolution crystal structure of the shaft pilin component SpaA from Corynebacterium diphtheriae, revealing both common and unique features. The SpaA pilin comprises 3 tandem Ig-like domains, with characteristic folds related to those typically found in non-pilus adhesins. Whereas both the middle and the C-terminal domains contain an intramolecular Lys-Asn isopeptide bond, previously detected in the shaft pilins of Streptococcus pyogenes and Bacillus cereus, the middle Ig-like domain also harbors a calcium ion, and the C-terminal domain contains a disulfide bond. By mass spectrometry, we show that the SpaA monomers are cross-linked in the assembled pili by a Lys-Thr isopeptide bond, as predicted by previous genetic studies. Together, our results reveal that despite profound dissimilarities in primary sequences, the shaft pilins of Gram-positive pathogens have strikingly similar tertiary structures, suggesting a modular backbone construction, including stabilizing intermolecular and intramolecular isopeptide bonds.

  • Organizational Affiliation

    Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1020, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative surface-anchored fimbrial subunitA [auth X]436Corynebacterium diphtheriaeMutation(s): 0 
Gene Names: SpaA
Find proteins for Q6NF81 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NF81 
Go to UniProtKB:  Q6NF81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NF81
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.78α = 90
b = 64.037β = 90
c = 199.192γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance