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Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex

Abstract

SCF complexes are the largest family of E3 ubiquitin–protein ligases and mediate the ubiquitination of diverse regulatory and signalling proteins. Here we present the crystal structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF complex, which shows that Cul1 is an elongated protein that consists of a long stalk and a globular domain. The globular domain binds the RING finger protein Rbx1 through an intermolecular β-sheet, forming a two-subunit catalytic core that recruits the ubiquitin-conjugating enzyme. The long stalk, which consists of three repeats of a novel five-helix motif, binds the Skp1–F boxSkp2 protein substrate-recognition complex at its tip. Cul1 serves as a rigid scaffold that organizes the Skp1–F boxSkp2 and Rbx1 subunits, holding them over 100 Å apart. The structure suggests that Cul1 may contribute to catalysis through the positioning of the substrate and the ubiquitin-conjugating enzyme, and this model is supported by Cul1 mutations designed to eliminate the rigidity of the scaffold.

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Figure 1: Overall structure of the Cul1–Rbx1–Skp1–F boxSkp2 quaternary complex.
Figure 2: Structural elements of the Cul1 N- and C-terminal domains (NTD and CTD).
Figure 3: Interactions between Rbx1 and the Cul1 CTD.
Figure 4: Cul1–Skp1–F boxSkp2 interface and the putative protein-binding site on other cullins.
Figure 5: The rigidity of the Cul1 scaffold is important for SCF E3 activity.
Figure 6: Model of the SCFSkp2–E2 complex.

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Acknowledgements

We thank H. Erdument-Bromage for N-terminal sequencing and mass spectroscopic analysis; T. Kamura and Z. Pan for reagents; members of the Pavletich laboratory for discussions; C. Murray for administrative assistance; and the staff of the National Synchrotron Light Source X9B beamline and of the Cornell High Energy Synchrotron Source MacCHESS for help with data collection. B.A.S. was supported by a special fellowship from the Leukemia and Lymphoma Society. This work was supported by the NIH, the Howard Hughes Medical Institute, the Dewitt Wallace Foundation, the Samuel and May Rudin Foundation, the Human Frontier Science Program Organization, the Welch Foundation, the Belfer Foundation and the Irma T. Hirschl Fundation.

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Correspondence to Nikola P. Pavletich.

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Zheng, N., Schulman, B., Song, L. et al. Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex. Nature 416, 703–709 (2002). https://doi.org/10.1038/416703a

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