3EIP

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

• PDB DOI: https://doi.org/10.2210/pdb3EIP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli str. K-12 substr. W3110
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 1999-03-29 Released: 1999-11-10 
• Deposition Author(s): Li, C., Zhao, D., Djebli, A., Shoham, M.

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Experimental Data Snapshot

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

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

• PubMed: 10574790 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.62 kDa 
• Atom Count: 1,505 
• Modelled Residue Count: 168 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLICIN E3 IMMUNITY PROTEIN)	A, B	84	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0
UniProt
Find proteins for P02984 (Escherichia coli) Explore P02984  Go to UniProtKB:  P02984

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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 = 80.07	α = 90
b = 53.72	β = 93.18
c = 36.25	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
SDMS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-10 
Deposition Author(s): Li, C., Zhao, D., Djebli, A., Shoham, M.

Revision History  

• 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