6TQD | pdb_00006tqd

D00-D0 domain of Intimin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TQD

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 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.

Macromolecule Content 

  • Total Structure Weight: 131.52 kDa 
  • Atom Count: 11,374 
  • Modeled Residue Count: 1,227 
  • Deposited Residue Count: 1,242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
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