3HR6 | pdb_00003hr6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.220 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 47.05 kDa 
  • Atom Count: 3,819 
  • Modeled Residue Count: 420 
  • Deposited Residue Count: 436 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative surface-anchored fimbrial subunit436Corynebacterium diphtheriaeMutation(s): 0 
Gene Names: SpaA
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.220 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.761α = 90
b = 63.683β = 90
c = 198.113γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

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
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary