Fig. 9: Degrader-dependent SMARCA2BD lysine densities in the CRL-VHL ubiquitination zone. | Nature Communications

Fig. 9: Degrader-dependent SMARCA2BD lysine densities in the CRL-VHL ubiquitination zone.

From: Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Fig. 9: Degrader-dependent SMARCA2BD lysine densities in the CRL-VHL ubiquitination zone.The alternative text for this image may have been generated using AI.

a Active form of CRL-VHL with bound SMARCA2BD and E2-ubiquitin in the open CRL conformation. Lysine residues on SMARCA2BD are highlighted in blue. b Same as panel a with a closed conformation of CRL generated by meta-eABF simulations. c Probability of distances of SMARCA2BD lysine residues (side-chain nitrogen atom) to the C-terminal glycine C atom of ubiquitin derived from ternary complex HREMD simulations with the three different degraders PROTAC 1, PROTAC 2, and ACBI1. d Density of lysine residues in 3D space near the ubiquitination zone of CRL-VHL. Source data are provided as a Source Data file.

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