8GSY | pdb_00008gsy

X-ray structure of Clostridium perfringens pili protein B N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb8GSY/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-07 Released: 2023-06-07 
• Deposition Author(s): Kamitori, S., Yamada, M., Tamai, E.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical characterization of Clostridium perfringens pili protein B collagen-binding domains.

Tamai, E., Yamada, M., Ishida, T., Arimura, N., Matsunami, R., Sekiya, H., Kamitori, S.

(2023) FEBS Lett 597: 1345-1354

• PubMed: 37071018 
• DOI: https://doi.org/10.1002/1873-3468.14626
• Primary Citation Related Structures: 
  8GSX, 8GSY


• PubMed Abstract: 
  

  Sortase-mediated pili are flexible rod proteins composed of major and minor/tip pilins, playing important roles in the initial adhesion of bacterial cells to host tissues. The pilus shaft is formed by covalent polymerization of major pilins, and the minor/tip pilin is covalently attached to the tip of the shaft involved in adhesion to the host cell. The Gram-positive bacterium Clostridium perfringens has a major pilin, and a minor/tip pilin (CppB) with the collagen-binding motif. Here, we report X-ray structures of CppB collagen-binding domains, collagen-binding assays and mutagenesis analysis, demonstrating that CppB collagen-binding domains adopt an L-shaped structure in open form, and that a small β-sheet unique to CppB provides a scaffold for a favourable binding site for collagen peptide.

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Organizational Affiliation: 
• Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, Japan.
Japan Aerospace Exploration Agency (JAXA), Ibaraki, Japan.
Research Facility Center for Science & Technology and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,092 
• Modeled Residue Count: 252 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan bound protein	A, B	144	Clostridium perfringens	Mutation(s): 0  Gene Names: NCTC8081_03081
UniProt
Find proteins for A0A2X3IRB0 (Clostridium perfringens) Explore A0A2X3IRB0  Go to UniProtKB:  A0A2X3IRB0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.08	α = 90
b = 39.08	β = 90
c = 290.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Kamitori, S., Yamada, M., Tamai, E.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06087

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description