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 9VO4 | pdb_00009vo4

X-ray structure of Clostridium perfringens pili CppB-CppA covalent complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 
    0.288 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9VO4

This is version 1.1 of the entry. See complete history. 

Literature

Dynamic motion of bacterial surface pili based on structural analyses of covalently linked complexes formed by tip and shaft pili proteins from Clostridium perfringens.

Nonaka, Y., Tamai, E., Sekiya, H., Kamitori, S.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70722
  • Primary Citation Related Structures: 
    9VO4, 9VO5, 9WME

  • PubMed Abstract: 

    The pathogenesis and infectivity of Gram-positive bacteria are mediated by many surface proteins covalently attached to the bacterial cell wall. Pili are types of surface appendages that play important roles in the initial adhesion of bacterial cells to host tissues and bacterial colonization. The Gram-positive bacterium Clostridium perfringens (C. perfringens), one of the pathogenic clostridial species causing gas gangrene and food poisoning, has sortase-mediated pili composed of shaft/major pilin A (CppA) and tip/minor pilin B (CppB). The pilus shaft is formed by covalent polymerization of CppA, and CppB is covalently attached to the tip of the shaft involved in adhesion to the host cell. The formation of covalent bonds between CppB and CppA, as well as between CppA and CppA, is catalyzed by class C sortase (CpSrtC), a member of the cysteine transpeptidase family. Since pili consistently have CppB at their tip, CpSrtC is the enzyme that preferentially catalyzes the attachment of CppB (tip) to CppA (shaft) rather than polymerization of CppAs by an unknown mechanism. We determined the structures of complexes formed by covalently linking CppB and CppA by X-ray crystallography and cryo-EM analysis. The complexes have an elongated structure in which β-sandwich folded domains are sequentially arranged, and an amide bond between Thr688 of CppB and Lys174 of CppA was clearly identified. The determined structures allowed us to construct a three-dimensional structure model with dynamic motion of C. perfringens pili, and proposed new insights into the mechanism by which CppB is preferentially attached to CppA.


  • Organizational Affiliation: 
    • Faculty of Medicine, Kagawa University, Japan.

Macromolecule Content 

  • Total Structure Weight: 248.93 kDa 
  • Atom Count: 15,092 
  • Modeled Residue Count: 1,909 
  • Deposited Residue Count: 2,220 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable surface protein
A, C
453Clostridium perfringens str. 13Mutation(s): 0 
Gene Names: CPE0156
UniProt
Find proteins for Q8XP10 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XP10 
Go to UniProtKB:  Q8XP10
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XP10
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SpaA-like prealbumin fold domain-containing protein
B, D
657Clostridium perfringens str. 13Mutation(s): 0 
Gene Names: CPE0155
UniProt
Find proteins for Q8XP11 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XP11 
Go to UniProtKB:  Q8XP11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XP11
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free:  0.288 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.88α = 90
b = 106.01β = 91.83
c = 191.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K04944

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release
  • Version 1.1: 2026-09-23
    Changes: Database references