3O0E

Crystal structure of OmpF in complex with colicin peptide OBS1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.014 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF.

Housden, N.G.Wojdyla, J.A.Korczynska, J.Grishkovskaya, I.Kirkpatrick, N.Brzozowski, A.M.Kleanthous, C.

(2010) Proc.Natl.Acad.Sci.USA 107: 21412-21417

  • DOI: 10.1073/pnas.1010780107

  • PubMed Abstract: 
  • The porins OmpF and OmpC are trimeric β-barrel proteins with narrow channels running through each monomer that exclude molecules > 600 Da while mediating the passive diffusion of small nutrients and metabolites across the Gram-negative outer membrane ...

    The porins OmpF and OmpC are trimeric β-barrel proteins with narrow channels running through each monomer that exclude molecules > 600 Da while mediating the passive diffusion of small nutrients and metabolites across the Gram-negative outer membrane (OM). Here, we elucidate the mechanism by which an entire soluble protein domain (> 6 kDa) is delivered through the lumen of such porins. Following high-affinity binding to the vitamin B(12) receptor in Escherichia coli, the bacteriocin ColE9 recruits OmpF or OmpC using an 83-residue intrinsically unstructured translocation domain (IUTD) to deliver a 16-residue TolB-binding epitope (TBE) in the center of the IUTD to the periplasm where it triggers toxin entry. We demonstrate that the IUTD houses two OmpF-binding sites, OBS1 (residues 2-18) and OBS2 (residues 54-63), which flank the TBE and bind with K(d)s of 2 and 24 μM, respectively, at pH 6.5 and 25 ºC. We show the two OBSs share the same binding site on OmpF and that the colicin must house at least one of them for antibiotic activity. Finally, we report the structure of the OmpF-OBS1 complex that shows the colicin bound within the porin lumen spanning the membrane bilayer. Our study explains how colicins exploit porins to deliver epitope signals to the bacterial periplasm and, more broadly, how the inherent flexibility and narrow cross-sectional area of an IUP domain can endow it with the ability to traverse a biological membrane via the constricted lumen of a β-barrel membrane protein.


    Organizational Affiliation

    Department of Biology, Area 10, and York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane porin 1a (Ia;b;F)
A, B, C, D, E, F
340Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ompF (cmlB, coa, cry, tolF)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpF Porin
Find proteins for P02931 (Escherichia coli (strain K12))
Go to UniProtKB:  P02931
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin-E9
L, M, N, O, P, Q
17Escherichia coliMutation(s): 0 
Gene Names: col (cei)
EC: 3.1.-.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpF Porin
Find proteins for P09883 (Escherichia coli)
Go to UniProtKB:  P09883
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download SDF File 
Download CCD File 
F
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.014 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.491α = 90.00
b = 101.618β = 94.46
c = 162.142γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
ADSCdata collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance