Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3

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Abstract

The centromere is a unique chromosomal locus that ensures accurate segregation of chromosomes during cell division by directing the assembly of a multiprotein complex, the kinetochore1. The centromere is marked by a conserved variant of conventional histone H3 termed CenH3 or CENP-A (ref. 2). A conserved motif of CenH3, the CATD, defined by loop 1 and helix 2 of the histone fold, is necessary and sufficient for specifying centromere functions of CenH3 (refs 3, 4). The structural basis of this specification is of particular interest. Yeast Scm3 and human HJURP are conserved non-histone proteins that interact physically with the (CenH3–H4)2 heterotetramer and are required for the deposition of CenH3 at centromeres in vivo5,6,7,8,9,10,11,12,13. Here we have elucidated the structural basis for recognition of budding yeast (Saccharomyces cerevisiae) CenH3 (called Cse4) by Scm3. We solved the structure of the Cse4-binding domain (CBD) of Scm3 in complex with Cse4 and H4 in a single chain model. An α-helix and an irregular loop at the conserved amino terminus and a shorter α-helix at the carboxy terminus of Scm3(CBD) wraps around the Cse4–H4 dimer. Four Cse4-specific residues in the N-terminal region of helix 2 are sufficient for specific recognition by conserved and functionally important residues in the N-terminal helix of Scm3 through formation of a hydrophobic cluster. Scm3(CBD) induces major conformational changes and sterically occludes DNA-binding sites in the structure of Cse4 and H4. These findings have implications for the assembly and architecture of the centromeric nucleosome.

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Figure 1: Overall structure of scSCH.
Figure 2: The N-terminal region (181–190) of the α2 helix of Cse4 is the Scm3 recognition motif.
Figure 3: Altered interactions in the CATD region in scSCH.
Figure 4: Scm3 induces large conformational changes in Cse4 and H4 and prevents loop 2 of H4 from binding to DNA.

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Protein Data Bank

Data deposits

The atomic coordinates have been deposited in the Protein Data Bank under accession code 2L5A.

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Acknowledgements

We thank J. Ying, K. Varney, J. F. Ellena and J. Gruschus for help collecting NMR spectra, A. Bax for discussion, C. Klee and M. Lichten for comments on the manuscript, and D. Cleveland for plasmids of human CENP-A and H4 histones. This work is supported by the intramural research programs of NCI, NIDDK and NHLBI.

Author information

Z.Z. and H.F. contributed equally to this work. Z.Z. performed protein engineering, biochemical and ITC studies. B.-R.Z. contributed to protein sample preparation. B.-R.Z. and L.M.M.J. contributed to the analysis of ITC data. H.F., K.H., A.Z. and N.T. collected the NMR spectra. H.F. and Z.Z. analysed the NMR data and H.F. solved the structure. R.G. performed the sedimentation experiments. H.X. provided initial plasmids and guidance in cloning. C.W. proposed the project and participated in manuscript writing. Y.B. contributed to the overall strategy, project management and writing of the manuscript. All authors read and commented on the manuscript.

Correspondence to Yawen Bai.

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Zhou, Z., Feng, H., Zhou, B. et al. Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3. Nature 472, 234–237 (2011) doi:10.1038/nature09854

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