Supplementary Figure 3: Analysis of the crystal packing of the Ube2V2–Ubc13~Ub–RING complex, revealing specificity for K63-linked polyubiquitination and electron density at ubiquitin Q62, K63 and E64.
From: Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains
The complex polymerises in the crystal such that Ub* (orange) from a symmetry related complex binds to Ube2V2 (dark blue), which orients Ub* such that K63 is presented to the isopeptide linked Ubc13~Ub conjugate.
(a) The crystal packing of three Ube2V2–Ubc13~Ub–RING complexes is shown.
Phases were generated from a molecular replacement solution, which had Q62, K63, and E64 deleted from both the acceptor ubiquitin (Ub*) and the donor ubiquitin. All b-factors were deleted and reset to single value of 20. The structure was refined with a single overall b-factor then refined again with individual b-factors.
(b) Difference electron density (Fo–Fc) contoured at 1.5σ is shown in dark blue for Ub*(orange).
(c) 2Fo–Fc electron density contoured at 0.5σ is shown in grey for Ub*.
(d) Difference electron density (Fo–Fc) contoured at 1.5σ is shown in dark blue for the donor ubiquitin (yellow). Ubc13 is coloured green and Ube2V2 is coloured blue.
(e) 2Fo–Fc electron density contoured at 0.5σ is shown in grey for the donor ubiquitin (yellow).
