PDB file 1RYP
This file depicts the structure of the yeast proteasome. Structure solved by M. Groll, L. Ditzel, J. Lowe, D. Stock, M. Bochtler, H. D. Bartunik, & R. Huber, in 1998.
Suggested display options:
Color chain to
distinguish the 28 different polypeptides. (Note that Chime does not have enough
colors to give each a different color.)
Select protein and display as spacefill.
Note the tight packing of the subunits.
Question: Is an opening visible by which proteins might enter the proteasome core complex to be degraded?
Visualize the location of the catalytic
N-terminal threonine residues, and the shape of the internal cavity.
With protein displayed as spacefill, select thr1 and color CPK. (With this file C atoms are yellowish. Or you can change the color of this residue to magenta, but it will then appear blue.)
One approach to examine the internal cavity is to orient the complex end on
(viewed from the end).
Then choose option - slab mode, and left-drag with the control key down.
Also try with the complex oriented in side view.
Alternatively you can remove a subunits from one end
to look inside.
Type in select *a, *b, *c, *d, *e, *f, *g and select hide.
Question: Are the catalytic threonine residues buried in the protein or exposed to the lumen?
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