1. Unveiling the Long-Held Secrets of the 26S Proteasome
Friedrich Förster, Pia Unverdorben, Paweł Śledź, Wolfgang Baumeister 
Structure 
Volume 21, Issue 9, Pages (September 2013)
DOI: /j.str
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2. Figure 1
Modular Architecture of ATP-Dependent Cytosolic Proteases Found in the Three Domains of Life
In all of these systems, the core is a two-fold symmetrical catalytic module of cylindrical shape (red) that is regulated by a hexameric AAA-ATPase ring (blue). HslV, the core module of the bacterial HslUV, is assembled of two identical homohexameric rings. The AAA-ATPase homohexamer HslU, which consists of a single AAA ring, caps both cylinder ends. ClpP is a homo 14-mer, to which the single AAA ring ClpX or the double AAA ring ClpA or ClpC can bind. Only bacteria of the order Actinomycetales have the CP-ARC system: an ATPase forming ring-shaped complexes (ARC), also referred to as Mycobacterium proteasomal ATPase (Mpa), regulates the four-ring CP. ARC consists of an AAA ring and two smaller stacked N rings. PAN from the archaeal CP-PAN system possesses only a single N ring. Strikingly, PAN is not conserved throughout archaea, and the double AAA ring Cdc48 is an alternative regulator of the CP. The AAA-ATPase module of the eukaryotic 26S proteasome is most closely related to PAN. Together with at least 13 different non-ATPase subunits (gray) it forms the RP, which associates to one or both ends of the eukaryotic CP.
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3. Figure 2
26S Proteasome Studied by Electron Microscopy over the Past Two Decades
(A) Two-dimensional averages from negatively stained Xenopus laevis 26S proteasomes allowed putting forward an assignment of functional modules in the 26S proteasome as early as 1993 that stood the test of time. Reproduced from Lupas et al. (1993).
(B) A three-dimensional reconstruction of the S. cerevisiae 26S proteasome at ∼7 Å resolution (left) allowed building an atomic model of the holocomplex (right) (Beck et al., 2012).
(C) In the cut-open view, the cavity system inside the unfoldase and CP can be discerned.
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4. Figure 3
Atomic Model of the 26S Proteasome and Its Sub-complexes (PDB code: 4b4t)
(Top) One half of the approximately C2-symmetrical holocomplex is shown from three different views, each rotated by 90°. Although the two halves are not exactly identical and C2 symmetry is broken, the differences are very subtle and ignored here. The CP is shown in red, the ATPase heterohexamer in blue, the PC subunits in brown (Rpn1) and yellow (Rpn2), the Ub receptors in purple, the PCI subunits in green, the N-terminal helix of Sem1/Rpn15 in orange, and unassigned helices in gray.
(Bottom) Close-up views of lid, including the semitransparent Rpn10 (left, view identical to top left) and base (right, view identical to top center).
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5. Figure 4
Crystal Structures of Three Major Representatives of RP Non-ATPases
(A) PC subunits. Rpn2 (PDB code: 4ADY) has of a torus-shaped central domain (orange) consisting of characteristic “PC repeats,” and the N-terminal (yellow) and C-terminal (red) segments form a rod-like domain.
(B) PCI subunits. From the N to C terminus, Rpn6 (left, PDB code: 3TXN) and Rpn12 (PDB code: 4B0Z) consist of TPR-like repeats (green) and a winged-helix (WH) domain (blue). The WH domain and adjacent conserved helices (light green) form the PCI module.
(C) MPN subunits. In the crystal, the catalytically inactive MPN domain of Rpn8 (PDB code: 2O95) forms a dimer (left) with a quaternary structure similar to that of the Rpn8/Rpn11 heterodimer. Rpn11’s active site likely resembles that of AMSH-LP (right, PDB code: 2ZNV), which involves a coordinated zinc ion and the binding of Ub (red) may be similar.
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6. Figure 5 Schematic of Modular Architecture of Base and Lid
(Left) Base. The N and AAA ring of the AAA-ATPase heterohexamer (Rpt1–Rpt6) are responsible for substrate unfolding. The tips of the Rpt coiled coils and the adjacent unfolded domains are probably involved in substrate commitment following initial recruitment by the Ub receptors. The non-ATPases Rpn1 and Rpn2 attached to the coiled coils of Rpt1/Rpt2 and Rpt6/Rpt3 are substrate-recruiting adaptors where Ub receptors (the resident receptor Rpn13, as well as the associated receptors Rad23, Dsk2, and Ddi1) and also the associated DUBs (Ubp6 and Uch37) can dock.
(Right) Lid. The DUB module comprising the MPN domains of Rpn8 and Rpn11 is in the center of the subcomplex. The C termini of the MPN and PCI subunits assemble to a helical bundle (gray) that serves as a tether in the lid. The WH domains of the PCI subunits form a horseshoe. The peptide Rpn15/Sem1 appears to “glue” Rpn7 and Rpn3 together. The TPR-like domains protrude from the horseshoe and facilitate interactions with the CP and possibly PIPs. The subunit Rpn10 is absent from both panels because it is not an integral part of either the purified base or the lid.
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7. Figure 6 Conformational Changes of the 26S Proteasome
The 26S proteasome has been imaged in the ATPh (left, EMDB: 2165), ATP-γS (middle, EMDB: 2348), and a substrate-engaged conformation (right, EMDB: 5669), seen from the top (top row) and side (middle). Atomic models (bottom) reveal a large conformational change between the ATPh (PDB code: 4B4T) and ATP-γS structures (PDB code: 4C0V) but little difference between the ATP-γS and substrate-engaged conformations. The ATP-γS structure (center) is colored according to the subunit types (see Figure 3), whereas the ATPh- and substrate-engaged structures are colored by their root-mean-square deviation (rmsd) with respect to the ATP-γS structure (bar indicates rmsd in Å).
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