3AN2: The Structure Of The Centromeric Nucleosome Containing Cenp-A

In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate alpha-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the alphaN helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome. A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg 80 and Gly 81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.
PDB ID: 3AN2Download
MMDB ID: 92122
PDB Deposition Date: 2010/8/27
Updated in MMDB: 2012/08
Experimental Method:
x-ray diffraction
Resolution: 3.6  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 3AN2: decameric; determined by author and by software (PISA)
Molecular Components in 3AN2
Label Count Molecule
Proteins (8 molecules)
Histone H3-like Centromeric Protein a(Gene symbol: CENPA)
Molecule annotation
Histone H4
Molecule annotation
Histone H2A Type 1-be(Gene symbol: HIST1H2AE)
Molecule annotation
Histone H2B Type 1-J(Gene symbol: HIST1H2BJ)
Molecule annotation
Nucleotide(1 molecule)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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