5AX6 | pdb_00005ax6

The crystal structure of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5AX6

This is version 1.3 of the entry. See complete history

Literature

Homo-trimeric Structure of the Type IVb Minor Pilin CofB Suggests Mechanism of CFA/III Pilus Assembly in Human Enterotoxigenic Escherichia coli

Kawahara, K.Oki, H.Fukakusa, S.Yoshida, T.Imai, T.Maruno, T.Kobayashi, Y.Motooka, D.Iida, T.Ohkubo, T.Nakamura, S.

(2016) J Mol Biology 428: 1209-1226

  • DOI: https://doi.org/10.1016/j.jmb.2016.02.003
  • Primary Citation Related Structures: 
    5AX6

  • PubMed Abstract: 

    In gram-negative bacteria, the assembly of type IV pilus (T4P) and the evolutionally related pseudopilus of type II secretion system involves specialized structural proteins called pilins and pseudopilins, respectively, and is dynamically regulated to promote bacterial pathogenesis. Previous studies have suggested that a structural "tip"-like hetero-complex formed through the interaction of at least three minor (pseudo) pilins plays an important role in this process, while some members of the pathogenic type IVb subfamily are known to have only one such minor pilin subunit whose function is still unknown. Here, we determined the crystal structure of the type IVb minor pilin CofB of colonization factor antigen/III from human enterotoxigenic Escherichia coli at 1.88-Å resolution. The crystal structure, in conjunction with physicochemical analysis in solution, reveals a symmetrical homo-trimeric arrangement distinct from the hetero-complexes of minor (pseudo) pilins observed in other T4P and type II secretion systems. Each CofB monomer adopts a unique three-domain architecture, in which the C-terminal β-sheet-rich lectin domain can effectively initiate trimer association of its pilin-like N-terminal domain through extensive hydrophobic interactions followed by domain swapping at the central hinge-like domain. Deletion of cofB produces a phenotype with no detectable pili formation on the cell surface, while molecular modeling indicates that the characteristic homo-trimeric structure of CofB is well situated at the pilus tip of colonization factor antigen/III formed by the major pilin CofA, suggesting a role for the minor pilin in the efficient initiation of T4P assembly.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 53.65 kDa 
  • Atom Count: 4,056 
  • Modeled Residue Count: 481 
  • Deposited Residue Count: 492 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CofB492Escherichia coliMutation(s): 0 
Gene Names: cofB
UniProt
Find proteins for Q93I73 (Escherichia coli)
Explore Q93I73 
Go to UniProtKB:  Q93I73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93I73
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT

Query on ACT



Download:Ideal Coordinates CCD File
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.948α = 90
b = 103.948β = 90
c = 364.474γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
ARPmodel building
SHELXDEphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary