Nucleosome Structure
David Marcey
© 2021

I. Introduction
II. The Histone Octamer
III. The DNA Superhelix
IV. References

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I. Introduction

The nucleosome core particle contains two copies of each histone protein (H2A, H2B, H3 and H4) and 146 basepairs (bp) of superhelical DNA wrapped around this histone octamer. It represents the first order of DNA packaging in the nucleus and as such is the principal structure that determines DNA accessibility.

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II. The Histone Octamer

Two copies of each histone protein, H2A, H2B, H3, and H4, are assembled into an octameric disc. Although each monomer has an N-terminal tail that projects from the histone core, the structure at left shows only a single tail from one H3 monomer.

All four histone proteins share a highly similar structural motif, the histone fold, comprising three alpha helices connected by two loops (shown here for H2A):
     alpha1-loop1-alpha2-loop2- alpha3.

The histone octomer consists of four histone heterodimers: two each of H3-H4 and H2A-H2B.

The histone fold motifs of the heterodimers are arranged with the loop1 of one monomer closely juxtaposed to the loop2 of the second monomer, shown here for a H3-H4 heterodimer. An axis of symmetry passes between the two long alpha2-helices of the two monomers.

The H3-H4 heterodimers pair to form a tetramer through interactions of a four-helix bundle (alpha2 and alpha3 of H3 from each dimer). The association of this (H3-H4)2 tetramer with DNA is the first step in nucleosome assembly.

Each H2A-H2B heterodimer binds to the (H3-H4)2 tetramer via another, homologous, four-helix bundle (alpha2 and alpha3 from both H2B and H4), joining the H2B and H4 histone folds.


 

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III. The DNA Superhelix

146 bp of double helical DNA are wrapped around the histone octamer in a superhelix.

A two-fold symmetry axis falls between the H3-H4 heterodimers and the H2A-H2B heterodimers.

This axis of symmetry intersects a single bp in the center of the superhelix, dividing the 146 bp DNA into 72 bp and 73 bp halves defined by the central bp.

The left-handed DNA superhelix wraps around the histone core in 1.65 turns.


 

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IV. References

Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature v389 pp.251-260 , 1997

 

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