Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.3 kDa 
• Atom Count: 2,137 
• Modelled Residue Count: 209 
• Deposited Residue Count: 212 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 3IGL

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 1)

• PDB DOI: 10.2210/pdb3IGL/pdb
• NDB: NA0106

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-28 Released: 2010-03-31 
• Deposition Author(s): Kitayner, M., Suad, O., Rozenberg, H., Shakked, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 

Literature

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B., Shakked, Z.

(2010) Nat Struct Mol Biol 17: 423-429

• PubMed: 20364130 
• DOI: 10.1038/nsmb.1800
• Primary Citation of Related Structures:  
  3IGK, 3IGL, 3KZ8


• PubMed Abstract: 
  

p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53-DNA complexes that show standard Watson-Crick base pairs, the newly reported structures show noncanonical Hoogsteen base-pairing geometry at the central A-T doublet of each half-site. Structural and computational analyses show that the Hoogsteen geometry distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential, which, together with the contiguous DNA configuration, results in enhanced protein-DNA and protein-protein interactions compared to noncontiguous half-sites. Our results suggest a mechanism relating spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of Hoogsteen base pairs as the basis for a novel mode of sequence readout.

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Organizational Affiliation: 

Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A	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
DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')	B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.161	α = 90
b = 49.841	β = 93.96
c = 33.962	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Kitayner, M., Suad, O., Rozenberg, H., Shakked, Z.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance