Structure of RCC1 chromatin factor bound to the nucleosome core particle

Abstract

The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin-bound RCC1 (regulator of chromosome condensation) protein, which recruits Ran to nucleosomes and activates Ran’s nucleotide exchange activity. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 Å resolution, providing an atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.

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Figure 1: Crystal structure of RCC1–nucleosome core particle complex.
Figure 2: Interactions of RCC1, LANA peptide and H4 peptide with the nucleosome histone dimer acidic patch.
Figure 3: Interactions between RCC1 and nucleosomal DNA.
Figure 4: The Widom 601 sequence forms a 145-bp nucleosome core particle.
Figure 5: Model for the Ran–RCC1–nucleosome core particle complex assuming no conformational changes.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited with the Protein Data Bank under accession code 3MVD.

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Acknowledgements

We thank M. Saxena for sharing unpublished coordinates of Drosophila RCC1; K. Wiley, D. Schlaich and M. Porzio for technical assistance; the staff of APS NE-CAT beamline 24-ID-E and Cornell CHESS beamlines A1 and F1 for their assistance during synchrotron data collection; N. Yennawar at the Penn Sate Huck Institutes X-ray core facility; W. Selleck, M. Adams, the members of the Tan laboratory and the Penn State Center for Eukaryotic Gene Regulation for discussions; T. Stukenberg for advice and encouragement at the initiation of this project, J. Widom for sending the 601 nucleosome DNA positioning sequence; and the Pew Scholar 20th Reunion Meeting for stimulating this project.

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R.D.M. cloned and purified macromolecules, crystallized, collected, processed X-ray data, refined and analysed the structure. J.R.E. performed pulldown assays and collected X-ray data. H.P.Y. collected and processed X-ray data. S.T. designed the study, cloned and purified macromolecules, crystallized, collected X-ray data, analysed the results and wrote the paper. All authors commented on the manuscript.

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Correspondence to Song Tan.

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Makde, R., England, J., Yennawar, H. et al. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562–566 (2010). https://doi.org/10.1038/nature09321

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