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protein Protein-protein interface(s) links
Immune system PDB id
1ujz
Jmol
Contents
Protein chains
87 a.a. *
127 a.a. *
Waters ×91
* Residue conservation analysis
PDB id:
1ujz
Name: Immune system
Title: Crystal structure of the e7_c/im7_c complex; a computationally designed interface between the colicin e7 dnase and the im7 immunity protein
Structure: Designed colicin e7 immunity protein. Chain: a. Synonym: dc immunity protein, im7. Engineered: yes. Mutation: yes. Designed colicin e7 dnase. Chain: b. Fragment: residues 446-573. Synonym: dc dnase.
Source: Escherichia coli. Organism_taxid: 562. Gene: ceie7. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.10Å     R-factor:   0.242     R-free:   0.270
Authors: T.Kortemme,L.A.Joachimiak,A.N.Bullock,A.D.Schuler, B.L.Stoddard,D.Baker
Key ref:
T.Kortemme et al. (2004). Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol, 11, 371-379. PubMed id: 15034550 DOI: 10.1038/nsmb749
Date:
13-Aug-03     Release date:   06-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03708  (IMM7_ECOLX) -  Colicin-E7 immunity protein
Seq:
Struc: 		87 a.a.
87 a.a.*
Protein chain
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
127 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytolysis   4 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1038/nsmb749 Nat Struct Mol Biol 11:371-379 (2004)
PubMed id: 15034550  
 
 
Computational redesign of protein-protein interaction specificity.
T.Kortemme, L.A.Joachimiak, A.N.Bullock, A.D.Schuler, B.L.Stoddard, D.Baker.
 
  ABSTRACT  
 
We developed a 'computational second-site suppressor' strategy to redesign specificity at a protein-protein interface and applied it to create new specifically interacting DNase-inhibitor protein pairs. We demonstrate that the designed switch in specificity holds in in vitro binding and functional assays. We also show that the designed interfaces are specific in the natural functional context in living cells, and present the first high-resolution X-ray crystallographic analysis of a computer-redesigned functional protein-protein interface with altered specificity. The approach should be applicable to the design of interacting protein pairs with novel specificities for delineating and re-engineering protein interaction networks in living cells.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. SPR sensograms. (a -c) A comparison of SPR sensograms for E7_B/Im7_B (a), E7_C/Im7_B (b) and E7_C/Im7_C (c) at concentrations of 100, 50, 30 and 20 nM immunity protein, demonstrating tight binding for the cognate E7_B/Im7_B and E7_C/Im7_C complexes and weaker binding for the noncognate E7_C/Im7_B complex. 		Figure 6.
Figure 6. The crystal structure of the E7_C/Im7_C complex. The DNase backbone is teal, the immunity protein gray. (a) 2F[o] - F[c] density around the designed residues is contoured at 1.3 (blue) and the density around the waters is contoured at a 1 (red). The B-factors for the displayed water molecules are 29 Å2 for water 24; 39 Å2 for water 18; and 43 Å2 for water 59 (the average B-factor for the waters in the structure is 36.85 Å2). (b) Overlay of the model (orange side chains) with the experimentally determined structure (yellow side chains). (c) Hydrogen bonding patterns in the experimentally determined structure (left) and the designed model (right). DNase C carbons are teal, immunity C carbons are gray.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 371-379) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.