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 5YPZ | pdb_00005ypz

Crystal structure of minor pilin CofB from CFA/III complexed with N-terminal peptide fragment of CofJ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YPZ

This is version 1.4 of the entry. See complete history. 

Literature

Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization.

Oki, H., Kawahara, K., Maruno, T., Imai, T., Muroga, Y., Fukakusa, S., Iwashita, T., Kobayashi, Y., Matsuda, S., Kodama, T., Iida, T., Yoshida, T., Ohkubo, T., Nakamura, S.

(2018) Proc Natl Acad Sci U S A 115: 7422-7427

  • DOI: https://doi.org/10.1073/pnas.1805671115
  • Primary Citation Related Structures: 
    5YPZ, 5YQ0

  • PubMed Abstract: 

    Initial attachment and subsequent colonization of the intestinal epithelium comprise critical events allowing enteric pathogens to survive and express their pathogenesis. In enterotoxigenic Escherichia coli (ETEC), these are mediated by a long proteinaceous fiber termed type IVb pilus (T4bP). We have reported that the colonization factor antigen/III (CFA/III), an operon-encoded T4bP of ETEC, possesses a minor pilin, CofB, that carries an H-type lectin domain at its tip. Although CofB is critical for pilus assembly by forming a trimeric initiator complex, its importance for bacterial attachment remains undefined. Here, we show that T4bP is not sufficient for bacterial attachment, which also requires a secreted protein CofJ, encoded within the same CFA/III operon. The crystal structure of CofB complexed with a peptide encompassing the binding region of CofJ showed that CofJ interacts with CofB by anchoring its flexible N-terminal extension to be embedded deeply into the expected carbohydrate recognition site of the CofB H-type lectin domain. By combining this structure and physicochemical data in solution, we built a plausible model of the CofJ-CFA/III pilus complex, which suggested that CofJ acts as a molecular bridge by binding both T4bP and the host cell membrane. The Fab fragments of a polyclonal antibody against CofJ significantly inhibited bacterial attachment by preventing the adherence of secreted CofJ proteins. These findings signify the interplay between T4bP and a secreted protein for attaching to and colonizing the host cell surface, potentially constituting a therapeutic target against ETEC infection.


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

Macromolecule Content 

  • Total Structure Weight: 168.24 kDa 
  • Atom Count: 11,241 
  • Modeled Residue Count: 1,473 
  • Deposited Residue Count: 1,548 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CofB
A, B, C
492Escherichia 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
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CofJ
D, E, F
24Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q93I65 (Escherichia coli)
Explore Q93I65 
Go to UniProtKB:  Q93I65
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93I65
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.216α = 90
b = 157.216β = 90
c = 118.132γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary