3EIP

CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase.

Li, C.Zhao, D.Djebli, A.Shoham, M.

(1999) Structure 7: 1365-1372

  • DOI: https://doi.org/10.1016/s0969-2126(00)80026-x
  • Primary Citation of Related Structures:  
    3EIP

  • PubMed Abstract: 

    Colicins are antibiotic-like proteins of Escherichia coli that kill related strains. Colicin E3 acts as an RNase that specifically cleaves 16S rRNA, thereby inactivating the ribosomes in the infected cell. The producing organism is protected against colicin E3 by a specific inhibitor, the immunity protein Im3, which forms a tight 1:1 complex with colicin E3 and renders it inactive. Crystallographic studies on colicin E3 and Im3 have been undertaken to unravel the structural basis for the ribonucleolytic activity and its inhibition. The crystal structure of Im3 has been determined to a resolution of 1.8 A. The structure consists of a four-standard antiparallel beta sheet flanked by three alpha helices on one side of the sheet. Thr7, Phe9, Phe16 and Phe74 form a hydrophobic cluster on the surface of the protein in the vicinity of Cys47. This cluster is part of a putative binding pocket which also includes nine polar residues. The putative binding pocket of Im3 is the probable site of interaction with colicin E3. The six acidic residues in the pocket may interact with some of the numerous basic residues of colicin E3. The involvement of hydrophobic moieties in the binding is consistent with the observation that the tight complex can only be dissociated by denaturation. The structure of Im3 resembles those of certain nucleic acid binding proteins, in particular domain II of topoisomerase I and RNA-binding proteins that contain the ribonucleoprotein (RNP) sequence motif. This observation suggests that Im3 has a nucleic acid binding function in addition to binding colicin E3.


  • Organizational Affiliation

    Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (COLICIN E3 IMMUNITY PROTEIN)
A, B
84Escherichia coli str. K-12 substr. W3110Mutation(s): 0 
UniProt
Find proteins for P02984 (Escherichia coli)
Explore P02984 
Go to UniProtKB:  P02984
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02984
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.07α = 90
b = 53.72β = 93.18
c = 36.25γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
SDMSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations