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PDBsum entry 3kmd

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protein dna_rna metals Protein-protein interface(s) links
DNA binding protein/DNA PDB id
3kmd
Jmol
Contents
Protein chains
200 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×523
* Residue conservation analysis
PDB id:
3kmd
Name: DNA binding protein/DNA
Title: Crystal structure of the p53 core domain bound to a full con site as a self-assembled tetramer
Structure: Cellular tumor antigen p53. Chain: a, b, d, c. Fragment: unp residues 92-291, DNA binding domain. Synonym: tumor suppressor p53, phosphoprotein p53, antigen 5'-d( Gp Gp Gp Cp Ap Tp Gp Cp Cp Tp Ap Gp Gp Cp A C)-3'. Chain: e, f. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes
Resolution:
2.15Å     R-factor:   0.217     R-free:   0.239
Authors: Y.Chen,R.Dey,L.Chen
Key ref: Y.Chen et al. (2010). Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. Structure, 18, 246-256. PubMed id: 20159469
Date:
10-Nov-09     Release date:   23-Feb-10    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 200 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     apoptotic process   2 terms 
  Biochemical function     transcription regulatory region DNA binding     3 terms  

 

 
Structure 18:246-256 (2010)
PubMed id: 20159469  
 
 
Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.
Y.Chen, R.Dey, L.Chen.
 
  ABSTRACT  
 
Recent studies suggest that p53 binds predominantly to consensus sites composed of two decameric half-sites with zero spacing in vivo. Here we report the crystal structure of the p53 core domain bound to a full consensus site as a tetramer at 2.13A resolution. Comparison with previously reported structures of p53 dimer:DNA complexes and a chemically trapped p53 tetramer:DNA complex reveals that DNA binding by the p53 core domain is a cooperative self-assembling process accompanied by structural changes of the p53 dimer and DNA. Each p53 monomer interacts with its two neighboring subunits through two different protein-protein interfaces. The DNA is largely B-form and shows no discernible bend, but the central base-pairs between the two half-sites display a significant slide. The extensive protein-protein and protein-DNA interactions explain the high cooperativity and kinetic stability of p53 binding to contiguous decameric sites and the conservation of such binding-site configuration in vivo.