1V74 | pdb_00001v74

Structure of the E. coli colicin D bound to its immunity protein ImmD

• PDB DOI: https://doi.org/10.2210/pdb1V74/pdb

• Classification: ANTIBIOTIC/IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12, Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-10 Released: 2004-03-30 
• Deposition Author(s): Graille, M., Mora, L., Buckingham, R.H., van Tilbeurgh, H., de Zamaroczy, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 

Literature

Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein

Graille, M., Mora, L., Buckingham, R.H., Van Tilbeurgh, H., De Zamaroczy, M.

(2004) EMBO J 23: 1474-1482

• PubMed: 15014439 
• DOI: https://doi.org/10.1038/sj.emboj.7600162
• Primary Citation Related Structures: 
  1V74


• PubMed Abstract: 
  

  Colicins are toxins secreted by Escherichia coli in order to kill their competitors. Colicin D is a 75 kDa protein that consists of a translocation domain, a receptor-binding domain and a cytotoxic domain, which specifically cleaves the anticodon loop of all four tRNA(Arg) isoacceptors, thereby inactivating protein synthesis and leading to cell death. Here we report the 2.0 A resolution crystal structure of the complex between the toxic domain and its immunity protein ImmD. Neither component shows structural homology to known RNases or their inhibitors. In contrast to other characterized colicin nuclease-Imm complexes, the colicin D active site pocket is completely blocked by ImmD, which, by bringing a negatively charged cluster in opposition to a positively charged cluster on the surface of colicin D, appears to mimic the tRNA substrate backbone. Site-directed mutations affecting either the catalytic domain or the ImmD protein have led to the identification of the residues vital for catalytic activity and for the tight colicin D/ImmD interaction that inhibits colicin D toxicity and tRNase catalytic activity.

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Organizational Affiliation: 
• LEBS, CNRS, UPR 9063, Gif sur Yvette, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.63 kDa 
• Atom Count: 1,780 
• Modeled Residue Count: 194 
• Deposited Residue Count: 194 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin D	A	107	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P17998 (Escherichia coli) Explore P17998  Go to UniProtKB:  P17998

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin D immunity protein	B	87	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P11899 (Escherichia coli) Explore P11899  Go to UniProtKB:  P11899

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.057	α = 90
b = 62.057	β = 90
c = 147.934	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Graille, M., Mora, L., Buckingham, R.H., van Tilbeurgh, H., de Zamaroczy, M.

Revision History  

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-03
  Changes: Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations