PDBsum entry 3exl

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protein dna_rna ligands metals links
Transcription/DNA PDB id
Protein chain
194 a.a. *
Waters ×161
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Crystal structure of a p53 core tetramer bound to DNA
Structure: Mouse p53 core domain. Chain: a. Engineered: yes. 5'- d( Dgp Dap Dgp Dcp Dap Dtp Dgp Dcp Dtp Dcp Da)-3'. Chain: c. Engineered: yes. Other_details: p53 consensus sequence. 5'-
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
2.20Å     R-factor:   0.202     R-free:   0.253
Authors: K.A.Malecka
Key ref: K.A.Malecka et al. (2009). Crystal structure of a p53 core tetramer bound to DNA. Oncogene, 28, 325-333. PubMed id: 18978813
16-Oct-08     Release date:   16-Dec-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02340  (P53_MOUSE) -  Cellular tumor antigen p53
387 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  


Oncogene 28:325-333 (2009)
PubMed id: 18978813  
Crystal structure of a p53 core tetramer bound to DNA.
K.A.Malecka, W.C.Ho, R.Marmorstein.
The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21464285 C.Chen, N.Gorlatova, Z.Kelman, and O.Herzberg (2011).
Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements.
  Proc Natl Acad Sci U S A, 108, 6456-6461.
PDB codes: 3qym 3qyn
21071400 I.Beno, K.Rosenthal, M.Levitine, L.Shaulov, and T.E.Haran (2011).
Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets.
  Nucleic Acids Res, 39, 1919-1932.  
21338609 N.Khazanov, and Y.Levy (2011).
Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains.
  J Mol Biol, 408, 335-355.  
21178074 R.Melero, S.Rajagopalan, M.Lázaro, A.C.Joerger, T.Brandt, D.B.Veprintsev, G.Lasso, D.Gil, S.H.Scheres, J.M.Carazo, A.R.Fersht, and M.Valle (2011).
Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA.
  Proc Natl Acad Sci U S A, 108, 557-562.  
21522129 T.J.Petty, S.Emamzadah, L.Costantino, I.Petkova, E.S.Stavridi, J.G.Saven, E.Vauthey, and T.D.Halazonetis (2011).
An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.
  EMBO J, 30, 2167-2176.
PDB codes: 3q01 3q05 3q06
  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.  
20696896 D.Coutandin, H.D.Ou, F.Löhr, and V.Dötsch (2010).
Tracing the protectors path from the germ line to the genome.
  Proc Natl Acad Sci U S A, 107, 15318-15325.  
20364130 M.Kitayner, H.Rozenberg, R.Rohs, O.Suad, D.Rabinovich, B.Honig, and Z.Shakked (2010).
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.
  Nat Struct Mol Biol, 17, 423-429.
PDB codes: 3igk 3igl 3kz8
20368720 S.Chitayat, and C.H.Arrowsmith (2010).
Four p(53)s in a pod.
  Nat Struct Mol Biol, 17, 390-391.  
20159469 Y.Chen, R.Dey, and L.Chen (2010).
Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.
  Structure, 18, 246-256.
PDB code: 3kmd
  20700496 Y.Pan, and R.Nussinov (2010).
Lysine120 interactions with p53 response elements can allosterically direct p53 organization.
  PLoS Comput Biol, 6, 0.  
19739284 G.V.Tolstonog, and W.Deppert (2009).
The p53 transcriptional synapse: activation on demand.
  Nat Struct Mol Biol, 16, 900-901.  
19629163 Y.Pan, and R.Nussinov (2009).
Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.
  PLoS Comput Biol, 5, e1000448.  
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.