3KMD

Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer

• PDB DOI:  https://doi.org/10.2210/pdb3KMD/pdb
• NAKB: 3KMD

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-11-10 Released: 2010-02-23 
• Deposition Author(s): Chen, Y., Dey, R., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.

Chen, Y., Dey, R., Chen, L.

(2010) Structure 18: 246-256

• PubMed: 20159469 
• DOI: https://doi.org/10.1016/j.str.2009.11.011
• Primary Citation of Related Structures:  
  3KMD


• PubMed 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.

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Organizational Affiliation: 

Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.07 kDa 
• Atom Count: 7,587 
• Modelled Residue Count: 838 
• Deposited Residue Count: 838 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B, C [auth D], D [auth C]	200	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3'	E, F	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth D], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.084	α = 90
b = 93.713	β = 90
c = 145.57	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Chen, Y., Dey, R., Chen, L.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description