1S32

Molecular Recognition of the Nucleosomal 'Supergroove'

Summary for 1S32

• Entry DOI: 10.2210/pdb1s32/pdb
• Related: 1AOI 1KX3 1KX5 1M18 1M19 1M1A
• Descriptor: palindromic alpha-satellite 146 bp DNA fragment, BETA-ALANINE, 3-AMINO-(DIMETHYLPROPYLAMINE), ... (14 entities in total)
• Functional Keywords: nucleosome core particle (ncp), pyrrole-imidazole (py-im) hairpin polyamide, clamp, nucleosome dynamics, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Cellular location: Nucleus: A0A310TTQ1
• Total number of polymer chains: 10
• Total formula weight: 200097.79

Authors

Edayathumangalam, R.S.,Weyermann, P.,Gottesfeld, J.M.,Dervan, P.B.,Luger, K. (deposition date: 2004-01-12, release date: 2004-05-11, Last modification date: 2023-11-15)

Primary citation

Edayathumangalam, R.S.,Weyermann, P.,Gottesfeld, J.M.,Dervan, P.B.,Luger, K.
Molecular Recognition of the Nucleosomal 'Supergroove'
Proc.Natl.Acad.Sci.USA, 101:6864-6869, 2004

PubMed Abstract: Chromatin is the physiological substrate in all processes involving eukaryotic DNA. By organizing 147 base pairs of DNA into two tight superhelical coils, the nucleosome generates an architecture where DNA regions that are 80 base pairs apart on linear DNA are brought into close proximity, resulting in the formation of DNA "supergrooves." Here, we report the design of a hairpin polyamide dimer that targets one such supergroove. The 2-A crystal structure of the nucleosome-polyamide complex shows that the bivalent "clamp" effectively crosslinks the two gyres of the DNA superhelix, improves positioning of the DNA on the histone octamer, and stabilizes the nucleosome against dissociation. Our findings identify nucleosomal supergrooves as platforms for molecular recognition of condensed eukaryotic DNA. In vivo, supergrooves may foster synergistic protein-protein interactions by bringing two regulatory elements into juxtaposition. Because supergroove formation is independent of the translational position of the DNA on the histone octamer, accurate nucleosome positioning over regulatory elements is not required for supergroove participation in eukaryotic gene regulation.

PubMed: 15100411
DOI: 10.1073/pnas.0401743101

Experimental method

X-RAY DIFFRACTION (2.05 Å)