REL PDBe PDBe PDBe 2015-05-05 2015-05-27 2015-08-12 2015-09-23 Bashore C Dambacher CM Matyskiela M Lander GC Martin A Proteasome, UPS, Ubp6, deubiquitinase, regulatory particle Bashore C Dambacher CM Goodall EA Matyskiela ME Lander GC Martin A NAT.STRUCT.MOL.BIOL. 22 712 719 2015 26301997 doi:10.1038/nsmb.3075 Yeast 26S proteasome in complex with ubiquitin-bound Ubp6 Yeast 26S proteasome in complex with ubiquitin-bound Ubp6

The sample was monodisperse

One to two 19S regulatory particles associates with the core particle to form a functional holoenzyme 2 1.5 1.5 26S proteasome Saccharomyces cerevisiae YYS40 Yeast Cytoplasm 1.5 1.5

50uM WT Ubp6 protein was reacted with 75uM ubiquitin vinyl sulfone at 37 degrees. Samples of 26S-bound Ubp6-UbVS were then diluted to ~25nM for analysis by negative stain electron microscopy.

1 Monomer false GO:0005838 IPR001353 ubiquitin-bound Ubp6 Saccharomyces cerevisiae baker's yeast 0.065 0.065

Recombinant Ubp6 was purified from E. coli by Ni affinity chromatography and SEC on a superdex 200. Ubp6-UbVS was made by incubating 75uM UbVS with 50uM Ubp6 at 37 degrees C for 7 hours. Ubp6-UbVS was added to holoenzymes at a 2:1 ratio and exchanged into 1mM ATPgS.

2 monomer true Escherichia coli BL21(DE3) P43593 singleParticle particle 0.05 7.6

60mM HEPES pH 7.6, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM TCEP, 1mM ATPgS

NEGATIVE

4 microliters of sample was applied to a freshly plasma-cleaned thin carbon surface pre-treated with 0.1% w/v poly-L-lysine hydrobromide. After removal of excess protein, negative staining was performed using 2% w/v uranyl formate solution.

400 mesh Cu-Rh Maxtaform grids were used following deposition of a thin continuous carbon film

NONE OTHER FEI TECNAI SPIRIT FLOOD BEAM BRIGHT FIELD LAB6 120 2.2 0.5 1.5 52000.0 52000.0 SIDE ENTRY, EUCENTRIC 294 297 295 Objective lens astigmatism was corrected using a quadrupole stigmator at 52,000 times magnification 2014-10-10 TVIPS TEMCAM-F416 (4k x 4k) 2.5 357 20

Automated imaging was performed using Leginon software

Room temperature, side entry holder 0 0

All image processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected using the Difference of Gaussians (DoG)-based automated particle picker from raw micrographs. The stack of particles was subjected to five iterations of 2D alignment and classification using multivariate statistical analysis (MSA) and multi-reference alignment (MRA). Selected 2D classes were used to generate a sub-stack that was subjected to twenty five iterations of 3D classification, requesting four classes using the Relion suite. Particles belonging to well-resolved 3D classes were used for further refinement by projection matching in Relion.

Phase flipping of whole micrographs

C2 OTHER 22.3 OTHER Relion

Final 3D models were refined using 12000 particles selected by combining two 3D classes from Relion processing

18565 4 4CR4 RIGID BODY FIT Chimera

An atomic model of yeast Ub-bound Ubp6 was constructed by superimposing the yeast Ubp6 crystal structure PDB 1VJV onto the stucture of the human Rsp14 structure bound to Ubiquitin PDB 2AYO, using the UCSF Chimera MatchMaker tool. These structures have high homology, and the resulting hybrid structure did not exhibit any clashes between the Ubiquitin and Ubp6. This Ubp6-Ub model was docked into the density putatively corresponding to Ubp6. PDB 4CR4 was used for docking other 26S core, base and lid subunits into the map, with the exception of the Rpn8-Rpn11 dimer, for which PDB 4O8Y was used. All docking of PDB structures was performed using the Fit in Map tool of UCSF Chimera

REAL