6TPL | pdb_00006tpl

D0-D1 domain of Intimin

• PDB DOI: https://doi.org/10.2210/pdb6TPL/pdb

• Classification: CELL ADHESION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2021-01-13 
• Deposition Author(s): Weikum, J., Leo, J.C., Morth, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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

• PubMed: 33277518 
• 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.

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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.
Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark.
Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800, Kgs. Lyngby, Denmark.
Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, 72076, Tübingen, Germany.
Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00, Lund, Sweden.
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316, Oslo, Norway. [e-mail].
Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK. [e-mail].
Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318, Oslo, Norway. [e-mail].
Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark. [e-mail].
Institute for Experimental Medical Research (IEMR), Oslo University Hospital, Ullevål, PB 4956, Nydalen, 0424, Oslo, Norway. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.2 kDa 
• Atom Count: 3,460 
• Modeled Residue Count: 393 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intimin	A, B	199	Escherichia coli	Mutation(s): 0  Gene Names: eae
UniProt
Find proteins for P19809 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore P19809  Go to UniProtKB:  P19809

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A], G [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.737	α = 97.076
b = 45.325	β = 97.55
c = 67.561	γ = 99.902

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Weikum, J., Leo, J.C., Morth, J.P.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description