2ZLD

Structure of OmpF co-crystallized with T83


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the OmpF porin: function in a colicin translocon.

Yamashita, E.Zhalnina, M.V.Zakharov, S.D.Sharma, O.Cramer, W.A.

(2008) EMBO J 27: 2171-2180

  • DOI: https://doi.org/10.1038/emboj.2008.137
  • Primary Citation of Related Structures:  
    2ZFG, 2ZLD

  • PubMed Abstract: 

    The OmpF porin in the Escherichia coli outer membrane (OM) is required for the cytotoxic action of group A colicins, which are proposed to insert their translocation and active domains through OmpF pores. A crystal structure was sought of OmpF with an inserted colicin segment. A 1.6 A OmpF structure, obtained from crystals formed in 1 M Mg2+, has one Mg2+ bound in the selectivity filter between Asp113 and Glu117 of loop 3. Co-crystallization of OmpF with the unfolded 83 residue glycine-rich N-terminal segment of colicin E3 (T83) that occludes OmpF ion channels yielded a 3.0 A structure with inserted T83, which was obtained without Mg2+ as was T83 binding to OmpF. The incremental electron density could be modelled as an extended poly-glycine peptide of at least seven residues. It overlapped the Mg2+ binding site obtained without T83, explaining the absence of peptide binding in the presence of Mg2+. Involvement of OmpF in colicin passage through the OM was further documented by immuno-extraction of an OM complex, the colicin translocon, consisting of colicin E3, BtuB and OmpF.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein F
A, B
340Escherichia coliMutation(s): 0 
Gene Names: ompFcmlBcoacrytolFb0929JW0912
Membrane Entity: Yes 
UniProt
Find proteins for P02931 (Escherichia coli (strain K12))
Explore P02931 
Go to UniProtKB:  P02931
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02931
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E3
C, D
7Escherichia coliMutation(s): 0 
EC: 3.1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.867α = 90
b = 116.867β = 90
c = 114.331γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description