8CPK | pdb_00008cpk

Crystal structure of EtpA secretion domain from Enterotoxigenic Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Literature

Structural and biophysical characterization of the secreted, beta-helical adhesin EtpA of Enterotoxigenic Escherichia coli.

Ntui, C.M.Fleckenstein, J.M.Schubert, W.D.

(2023) PLoS One 18: e0287100-e0287100

  • DOI: https://doi.org/10.1371/journal.pone.0287100
  • Primary Citation Related Structures: 
    8CPK

  • PubMed Abstract: 

    Enterotoxigenic Escherichia coli (ETEC) is a diarrhoeal pathogen associated with high morbidity and mortality especially among young children in developing countries. At present, there is no vaccine for ETEC. One candidate vaccine antigen, EtpA, is a conserved secreted adhesin that binds to the tips of flagellae to bridge ETEC to host intestinal glycans. EtpA is exported through a Gram-negative, two-partner secretion system (TPSS, type Vb) comprised of the secreted EtpA passenger (TpsA) protein and EtpB (TpsB) transporter that is integrated into the outer bacterial membrane. TpsA proteins share a conserved, N-terminal TPS domain followed by an extensive C-terminal domain with divergent sequence repeats. Two soluble, N-terminal constructs of EtpA were prepared and analysed respectively including residues 67 to 447 (EtpA67-447) and 1 to 606 (EtpA1-606). The crystal structure of EtpA67-447 solved at 1.76 Å resolution revealed a right-handed parallel β-helix with two extra-helical hairpins and an N-terminal β-strand cap. Analyses by circular dichroism spectroscopy confirmed the β-helical fold and indicated high resistance to chemical and thermal denaturation as well as rapid refolding. A theoretical AlphaFold model of full-length EtpA largely concurs with the crystal structure adding an extended β-helical C-terminal domain after an interdomain kink. We propose that robust folding of the TPS domain upon secretion provides a template to extend the N-terminal β-helix into the C-terminal domains of TpsA proteins.


  • Organizational Affiliation
    • Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.

Macromolecule Content 

  • Total Structure Weight: 155.39 kDa 
  • Atom Count: 12,252 
  • Modeled Residue Count: 1,533 
  • Deposited Residue Count: 1,536 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EtpA
A, B, C, D
384Escherichia coliMutation(s): 1 
Gene Names: etpA
UniProt
Find proteins for Q29XT7 (Escherichia coli)
Explore Q29XT7 
Go to UniProtKB:  Q29XT7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ29XT7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.711α = 91.61
b = 64.188β = 90.89
c = 123.957γ = 90.02
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI089894

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references