3SOK | pdb_00003sok

Dichelobacter nodosus pilin FimA

• PDB DOI: https://doi.org/10.2210/pdb3SOK/pdb

• Classification: CELL ADHESION
• Organism(s): Dichelobacter nodosus
• Expression System: Pseudomonas aeruginosa PAK
• Mutation(s): No 
• Membrane Protein: Yes  OPMMemProtMD


• Deposited: 2011-06-30 Released: 2011-11-02 
• Deposition Author(s): Arvai, A.S., Craig, L., Hartung, S., Wood, T., Kolappan, S., Shin, D.S., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Ultrahigh Resolution and Full-length Pilin Structures with Insights for Filament Assembly, Pathogenic Functions, and Vaccine Potential.

Hartung, S., Arvai, A.S., Wood, T., Kolappan, S., Shin, D.S., Craig, L., Tainer, J.A.

(2011) J Biological Chem 286: 44254-44265

• PubMed: 22027840 
• DOI: https://doi.org/10.1074/jbc.M111.297242
• Primary Citation Related Structures: 
  3SOJ, 3SOK


• PubMed Abstract: 
  

  Pilin proteins assemble into Type IV pili (T4P), surface-displayed bacterial filaments with virulence functions including motility, attachment, transformation, immune escape, and colony formation. However, challenges in crystallizing full-length fiber-forming and membrane protein pilins leave unanswered questions regarding pilin structures, assembly, functions, and vaccine potential. Here we report pilin structures of full-length DnFimA from the sheep pathogen Dichelobacter nodosus and FtPilE from the human pathogen Francisella tularensis at 2.3 and 1 Å resolution, respectively. The DnFimA structure reveals an extended kinked N-terminal α-helix, an unusual centrally located disulfide, conserved subdomains, and assembled epitopes informing serogroup vaccines. An interaction between the conserved Glu-5 carboxyl oxygen and the N-terminal amine of an adjacent subunit in the crystallographic dimer is consistent with the hypothesis of a salt bridge between these groups driving T4P assembly. The FtPilE structure identifies an authentic Type IV pilin and provides a framework for understanding the role of T4P in F. tularensis virulence. Combined results define a unified pilin architecture, specialized subdomain roles in pilus assembly and function, and potential therapeutic targets.

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Organizational Affiliation: 
• Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037.
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada. Electronic address: [e-mail].
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.22 kDa 
• Atom Count: 2,272 
• Modeled Residue Count: 293 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fimbrial protein	A, B	151	Dichelobacter nodosus	Mutation(s): 0  Gene Names: fimA Membrane Entity: Yes
UniProt
Find proteins for P02975 (Dichelobacter nodosus) Explore P02975  Go to UniProtKB:  P02975

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.729	α = 90
b = 105.729	β = 90
c = 73.848	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Arvai, A.S., Craig, L., Hartung, S., Wood, T., Kolappan, S., Shin, D.S., Tainer, J.A.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2012-01-04
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary