1JCH

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.

Soelaiman, S., Jakes, K., Wu, N., Li, C., Shoham, M.

(2001) Mol Cell 8: 1053-1062

  • DOI: 10.1016/s1097-2765(01)00396-3
  • Primary Citation of Related Structures:  
    1JCH

  • PubMed Abstract: 

    • Colicins kill E. coli by a process that involves binding to a surface receptor, entering the cell, and, finally, intoxicating it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3, reported here in a binary complex with its immunity protein (IP), reveals a Y-shaped molecule with the receptor binding domain forming a 100 A long stalk and the two globular heads of the translocation domain (T) and the catalytic domain (C) comprising the two arms ...

    Colicins kill E. coli by a process that involves binding to a surface receptor, entering the cell, and, finally, intoxicating it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3, reported here in a binary complex with its immunity protein (IP), reveals a Y-shaped molecule with the receptor binding domain forming a 100 A long stalk and the two globular heads of the translocation domain (T) and the catalytic domain (C) comprising the two arms. Active site residues are D510, H513, E517, and R545. IP is buried between T and C. Rather than blocking the active site, IP prevents access of the active site to the ribosome.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLICIN E3A, C551Escherichia coli str. K-12 substr. W3110Mutation(s): 0 
EC: 3.1.21 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P00646 (Escherichia coli)
Explore P00646 
Go to UniProtKB:  P00646
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00646
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COLICIN E3 IMMUNITY PROTEINB, D84Escherichia 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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.986α = 90
b = 195.733β = 113.22
c = 85.124γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance