IndraLab
Statements
reach
"After transferring Zn ion to the Rpn11, we used both the Rpn11 monomer (Figure 2A) and the Rpn8-Rpn11 heterodimer (Figure 3A) structures for subsequent analysis.For the CSN5 monomer (Figure 2B), the recently solved crystal structure of CSN5 with CSN5i-3 (PDB_code: 5JOG) (Schlierf et al., 2016) was considered."
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"Indeed, although the Rpn11/Rpn8 heterodimer has not been observed to accumulate appreciably in cells, substantial free lid has been observed [51], necessitating some regulatory mechanism to prevent spurious deubiquitination.Cryo-EM demonstrated that Rpn11 exists in an inhibited form in the isolated lid that explains these biochemical observations (Figure 6) [83]."
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"Thus, we investigated whether this was an unrealistic over binding, a protein-protein complex environment would be able to reproduce the selectivity.In the heterodimeric Rpn8-Rpn11 complex, CSN5i-3 binding in the pocket was not stable (Figure 7C), the distance to zinc increases continously and eventually the ligand lost coordination with Zn (Figure 7D and Table 1) which shows that the influence of Rpn8 on the capzimin bound Rpn11 is prominent."
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"Both crystal structures of the yeast Rpn8-Rpn11 heterodimer (Pathare et al., 2014) and the cryo-EM structure of human 26S proteasome (Huang et al., 2016) show that the α2 helices of both proteins makes extensive contacts with each other.Molecular dynamics simulations refined the binding position of capzimin."
sparser
"Systematic evaluation of PSMD1-14 expression revealed significant upregulation (p<0.05) of PSMD1, PSMD2, PSMD3, PSMD4, PSMD7-PSMD14 transcripts in pancreatic tumor tissues compared with adjacent normal controls, with the notable exception of PSMD6 which demonstrated reduced mRNA expression ( xref )."