PDBsum entry 2ocj

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protein metals Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
194 a.a. *
_ZN ×4
Waters ×389
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Human p53 core domain in the absence of DNA
Structure: P53 tumor suppressor. Chain: a, b, c, d. Fragment: core domain (residues 94-312). Synonym: tumor suppressor p53, phosphoprotein p53, antigen ny-co-13. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.05Å     R-factor:   0.209     R-free:   0.246
Authors: Y.Wang,A.Rosengarth,H.Luecke
Key ref:
Y.Wang et al. (2007). Structure of the human p53 core domain in the absence of DNA. Acta Crystallogr D Biol Crystallogr, 63, 276-281. PubMed id: 17327663 DOI: 10.1107/S0907444906048499
20-Dec-06     Release date:   06-Mar-07    
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Protein chains
Pfam   ArchSchema ?
P04637  (P53_HUMAN) -  Cellular tumor antigen p53
393 a.a.
194 a.a.
Key:    PfamA domain  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  


DOI no: 10.1107/S0907444906048499 Acta Crystallogr D Biol Crystallogr 63:276-281 (2007)
PubMed id: 17327663  
Structure of the human p53 core domain in the absence of DNA.
Y.Wang, A.Rosengarth, H.Luecke.
The tumor suppressor protein p53 plays a key role in cell-cycle regulation by triggering DNA repair, cell-cycle arrest and apoptosis when the appropriate signal is received. p53 has the classic architecture of a transcription factor, with an amino-terminal transactivation domain, a core DNA-binding domain and carboxy-terminal tetramerization and regulatory domains. The crystal structure of the p53 core domain, which includes the amino acids from residue 96 to residue 289, has been determined in the absence of DNA to a resolution of 2.05 A. Crystals grew in a new monoclinic space group (P2(1)), with unit-cell parameters a = 68.91, b = 69.36, c = 84.18 A, beta = 90.11 degrees . The structure was solved by molecular replacement and has been refined to a final R factor of 20.9% (R(free) = 24.6%). The final model contains four molecules in the asymmetric unit with four zinc ions and 389 water molecules. The non-crystallographic tetramers display different protein contacts from those in other p53 crystals, giving rise to the question of how p53 arranges as a tetramer when it binds its target DNA.
  Selected figure(s)  
Figure 1.
Figure 1 Schematic ribbon diagram of the overall structure of the p53 core domain in the absence of DNA. The zinc ion is highlighted in dark gray near loop L3.
Figure 2.
Figure 2 Backbone superposition of the four molecules in the asymmetric unit of the p53 core domain in the absence of DNA. Molecule A, yellow; molecule B, purple; molecule C, pink; molecule D, green. The region with the most significant structural variation is the turn between S7 and S8, which is encircled by a blue dashed line.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 276-281) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472523 J.Scotcher, D.J.Clarke, S.K.Weidt, C.L.Mackay, T.R.Hupp, P.J.Sadler, and P.R.Langridge-Smith (2011).
Identification of two reactive cysteine residues in the tumor suppressor protein p53 using top-down FTICR mass spectrometry.
  J Am Soc Mass Spectrom, 22, 888-897.  
  20516128 A.C.Joerger, and A.R.Fersht (2010).
The tumor suppressor p53: from structures to drug discovery.
  Cold Spring Harb Perspect Biol, 2, a000919.  
20113312 A.Merabet, H.Houlleberghs, K.Maclagan, E.Akanho, T.T.Bui, B.Pagano, A.F.Drake, F.Fraternali, and P.V.Nikolova (2010).
Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights.
  Biochem J, 427, 225-236.  
18978813 K.A.Malecka, W.C.Ho, and R.Marmorstein (2009).
Crystal structure of a p53 core tetramer bound to DNA.
  Oncogene, 28, 325-333.
PDB codes: 3exj 3exl
19515728 K.H.Khoo, A.C.Joerger, S.M.Freund, and A.R.Fersht (2009).
Stabilising the DNA-binding domain of p53 by rational design of its hydrophobic core.
  Protein Eng Des Sel, 22, 421-430.
PDB code: 2wgx
19748724 Y.H.Tan, Y.M.Chen, X.Ye, Q.Lu, V.Tretyachenko-Ladokhina, W.Yang, D.F.Senear, and R.Luo (2009).
Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations.
  Biophys Chem, 145, 37-44.  
18410249 A.C.Joerger, and A.R.Fersht (2008).
Structural biology of the tumor suppressor p53.
  Annu Rev Biochem, 77, 557-582.  
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.