6TQD

D00-D0 domain of Intimin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action.

Weikum, J.Kulakova, A.Tesei, G.Yoshimoto, S.Jaegerum, L.V.Schutz, M.Hori, K.Skepo, M.Harris, P.Leo, J.C.Morth, J.P.

(2020) Sci Rep 10: 21249-21249

  • DOI: https://doi.org/10.1038/s41598-020-77706-7
  • Primary Citation of Related Structures:  
    6TPL, 6TQD

  • PubMed Abstract: 

    Enterohemorrhagic and enteropathogenic Escherichia coli are among the most important food-borne pathogens, posing a global health threat. The virulence factor intimin is essential for the attachment of pathogenic E. coli to the intestinal host cell. Intimin consists of four extracellular bacterial immunoglobulin-like (Big) domains, D00-D2, extending into the fifth lectin subdomain (D3) that binds to the Tir-receptor on the host cell. Here, we present the crystal structures of the elusive D00-D0 domains at 1.5 Å and D0-D1 at 1.8 Å resolution, which confirms that the passenger of intimin has five distinct domains. We describe that D00-D0 exhibits a higher degree of rigidity and D00 likely functions as a juncture domain at the outer membrane-extracellular medium interface. We conclude that D00 is a unique Big domain with a specific topology likely found in a broad range of other inverse autotransporters. The accumulated data allows us to model the complete passenger of intimin and propose functionality to the Big domains, D00-D0-D1, extending directly from the membrane.


  • Organizational Affiliation

    Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318, Oslo, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intimin
A, B, C, D, E
A, B, C, D, E, F
207Escherichia coli O127:H6 str. E2348/69Mutation(s): 0 
Gene Names: eaeeaeAE2348C_3939
UniProt
Find proteins for P19809 (Escherichia coli O127:H6 (strain E2348/69 / EPEC))
Explore P19809 
Go to UniProtKB:  P19809
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19809
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
T [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
M [auth B]
N [auth B]
Q [auth C]
G [auth A],
H [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
W [auth E],
X [auth F]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
P [auth B]
S [auth C]
J [auth A],
K [auth A],
L [auth A],
P [auth B],
S [auth C],
V [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.039α = 77.776
b = 65.473β = 76.55
c = 79.378γ = 84.762
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description