Editing Proteasome (section)

===19S regulatory particle===
The 19S particle in eukaryotes consists of 19 individual proteins and is divisible into two subassemblies, a 9-subunit base that binds directly to the α ring of the 20S core particle, and a 10-subunit lid. Six of the nine base proteins are ATPase subunits from the AAA Family, and an evolutionary homolog of these ATPases exists in archaea, called PAN (proteasome-activating nucleotidase).<ref>{{cite journal | vauthors = Zwickl P, Ng D, Woo KM, Klenk HP, Goldberg AL | title = An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes | journal = The Journal of Biological Chemistry | volume = 274 | issue = 37 | pages = 26008–14 | date = September 1999 | pmid = 10473546 | doi = 10.1074/jbc.274.37.26008 | doi-access = free }}</ref> The association of the 19S and 20S particles requires the binding of ATP to the 19S ATPase subunits, and ATP hydrolysis is required for the assembled complex to degrade folded and ubiquitinated proteins. Note that only the step of substrate unfolding requires energy from ATP hydrolysis, while ATP-binding alone can support all the other steps required for protein degradation (e.g., complex assembly, gate opening, translocation, and proteolysis).<ref name="Smith">{{cite journal | vauthors = Smith DM, Kafri G, Cheng Y, Ng D, Walz T, Goldberg AL | title = ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins | journal = Molecular Cell | volume = 20 | issue = 5 | pages = 687–98 | date = December 2005 | pmid = 16337593 | doi = 10.1016/j.molcel.2005.10.019 | doi-access = free }}</ref><ref name="Liu"/> In fact, ATP binding to the ATPases by itself supports the rapid degradation of unfolded proteins. However, while ATP hydrolysis is required for unfolding only, it is not yet clear whether this energy may be used in the coupling of some of these steps.<ref name=Liu>{{cite journal | vauthors = Liu CW, Li X, Thompson D, Wooding K, Chang TL, Tang Z, Yu H, Thomas PJ, DeMartino GN | title = ATP binding and ATP hydrolysis play distinct roles in the function of 26S proteasome | journal = Molecular Cell | volume = 24 | issue = 1 | pages = 39–50 | date = October 2006 | pmid = 17018291 | doi = 10.1016/j.molcel.2006.08.025 | pmc = 3951175 }}</ref><ref>{{cite journal | vauthors = Lam YA, Lawson TG, Velayutham M, Zweier JL, Pickart CM | title = A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal | journal = Nature | volume = 416 | issue = 6882 | pages = 763–7 | date = April 2002 | pmid = 11961560 | doi = 10.1038/416763a | bibcode = 2002Natur.416..763L | s2cid = 4421764 }}</ref>

[[File:26S proteasome structure.jpg|thumb|right|Cartoon representation of the 26S proteasome.<ref name=Beck>{{cite journal | vauthors = Beck F, Unverdorben P, Bohn S, Schweitzer A, Pfeifer G, Sakata E, Nickell S, Plitzko JM, Villa E, Baumeister W, Förster F | title = Near-atomic resolution structural model of the yeast 26S proteasome | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 37 | pages = 14870–5 | date = September 2012 | pmid = 22927375 | doi = 10.1073/pnas.1213333109 | pmc=3443124| bibcode = 2012PNAS..10914870B | doi-access = free }}</ref>]]

In 2012, two independent efforts have elucidated the molecular architecture of the 26S proteasome by [[single particle analysis|single particle electron microscopy]].<ref name=Lander>{{cite journal | vauthors = Lander GC, Estrin E, Matyskiela ME, Bashore C, Nogales E, Martin A | title = Complete subunit architecture of the proteasome regulatory particle | journal = Nature | volume = 482 | issue = 7384 | pages = 186–91 | date = February 2012 | pmid = 22237024 | pmc = 3285539| doi = 10.1038/nature10774 | bibcode = 2012Natur.482..186L }}</ref><ref name=Lasker>{{cite journal | vauthors = Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W | title = Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 5 | pages = 1380–7 | date = January 2012 | pmid = 22307589 | doi = 10.1073/pnas.1120559109 | pmc=3277140| doi-access = free | bibcode = 2012PNAS..109.1380L }}</ref> In 2016, three independent efforts have determined the first near-atomic resolution structure of the human 26S proteasome in the absence of substrates by cryo-EM.<ref name=Chen>{{cite journal | vauthors = Chen S, Wu J, Lu Y, Ma YB, Lee BH, Yu Z, Ouyang Q, Finley DJ, Kirschner MW, Mao Y | title = Structural basis for dynamic regulation of the human 26S proteasome | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 46 | pages = 12991–12996 | date = November 2016 | pmid = 27791164 | pmc = 5135334 | doi = 10.1073/pnas.1614614113 | bibcode = 2016PNAS..11312991C | doi-access = free }}</ref><ref name=Huang>{{cite journal | vauthors = Huang X, Luan B, Wu J, Shi Y | title = An atomic structure of the human 26S proteasome | journal = Nature Structural & Molecular Biology | volume = 23 | issue = 9 | pages = 778–785 | date = September 2016 | pmid = 27428775 | doi = 10.1038/nsmb.3273 | s2cid = 21909333 }}</ref><ref name=Schweitzer>{{cite journal | vauthors = Schweitzer A, Aufderheide A, Rudack T, Beck F, Pfeifer G, Plitzko JM, Sakata E, Schulten K, Förster F, Baumeister W | title = Structure of the human 26S proteasome at a resolution of 3.9 Å | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 28 | pages = 7816–7821 | date = July 2016 | pmid = 27791164 | pmc = 5135334 | doi = 10.1073/pnas.1614614113 | bibcode = 2016PNAS..11312991C | doi-access = free }}</ref>  In the heart of the 19S, directly adjacent to the 20S, are the AAA-ATPases ([[AAA proteins]]) that assemble to a heterohexameric ring of the order Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5. This ring is a trimer of dimers: Rpt1/Rpt2, Rpt6/Rpt3, and Rpt4/Rpt5 dimerize via their N-terminal coiled-coils. These coiled-coils protrude from the hexameric ring. The largest regulatory particle non-ATPases Rpn1 and Rpn2 bind to the tips of Rpt1/2 and Rpt6/3, respectively. The ubiquitin receptor Rpn13 binds to Rpn2 and completes the base sub-complex. The lid covers one half of the AAA-ATPase hexamer (Rpt6/Rpt3/Rpt4) and, unexpectedly, directly contacts the 20S via Rpn6 and to lesser extent Rpn5. The subunits Rpn9, Rpn5, Rpn6, Rpn7, Rpn3, and Rpn12, which are structurally related among themselves and to subunits of the [[COP9 signalosome|COP9 complex]] and [[Eukaryotic initiation factor 3|eIF3]] (hence called PCI subunits) assemble to a horseshoe-like structure enclosing the Rpn8/Rpn11 heterodimer. Rpn11, the [[deubiquitinating enzyme]], is placed at the mouth of the AAA-ATPase hexamer, ideally positioned to remove ubiquitin moieties immediately before translocation of substrates into the 20S. The second ubiquitin receptor identified to date, Rpn10, is positioned at the periphery of the lid, near subunits Rpn8 and Rpn9.

==== Conformational changes of 19S ====
These initial structures showed that the 19S RP adopted a number of states (termed s1, s2, s3, and s4 in yeast) which provided a model for how substrates were recruited and subsequently degraded by the proteasome.<ref name="Unverdorben">{{cite journal |vauthors=Unverdorben P, Beck F, Śledź P, Schweitzer A, Pfeifer G, Plitzko JM, Baumeister W, Förster F |date=April 2014 |title=Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=111 |issue=15 |pages=5544–9 |bibcode=2014PNAS..111.5544U |doi=10.1073/pnas.1403409111 |pmc=3992697 |pmid=24706844 |doi-access=free}}</ref><ref name="Matyskiela">{{cite journal |vauthors=Matyskiela ME, Lander GC, Martin A |date=July 2013 |title=Conformational switching of the 26S proteasome enables substrate degradation |journal=Nature Structural & Molecular Biology |volume=20 |issue=7 |pages=781–788 |doi=10.1038/nsmb.2616 |pmc=3712289 |pmid=23770819}}</ref>  A hallmark of the AAA-ATPase configuration in this predominant low-energy state is a staircase- or lockwasher-like arrangement of the AAA-domains.<ref name="Beck" /><ref name="Lander" />   These states could be manipulated upon the addition of ATPgS,<ref name="Sledz" /> substrate, or by the non-essential DUB Ubp6.  The s1 state was proposed to be the resting state of the proteasome, allowing for a protein substrate to engage the AAA motor.  Upon binding a substrate, the proteasome would shift to a processing state, in which a central channel from the top of the AAA motor into the 20S proteolytic chamber would form allowing a direct passage of a substrate from the 19S RP into the proteolytic site.   Subsequent studies with the human proteasome have shown many more sub-states, and provide a model for ATP dependent translocation of a substrate.<ref name="Zhuy">{{cite journal |vauthors=Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y, Mao Y |date=April 2018 |title=Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome |journal=Nature Communications |volume=9 |issue=1 |page=1360 |bibcode=2018NatCo...9.1360Z |doi=10.1038/s41467-018-03785-w |pmc=5893597 |pmid=29636472}}</ref><ref name="Chen" /><ref name="Dong" />

In 2018, the first structure of a processing proteasome bound to a substrate was solved using cryo-EM, confirming biochemistry that showed that de-ubiquitination by Rpn11 was performed in a translocation dependent manner <ref name=":0">{{cite journal |last1=Worden |first1=Evan J. |last2=Dong |first2=Ken C. |last3=Martin |first3=Andreas |title=An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome |journal=Molecular Cell |date=September 2017 |volume=67 |issue=5 |pages=799–811.e8 |doi=10.1016/j.molcel.2017.07.023|pmid=28844860 }}</ref> and revealing key steps in translocation.<ref name="Substrate-engaged 26 S proteasome s"/>  Subsequently, a major effort has elucidated the detailed structures of deubiquitylation, initiation of translocation and processive unfolding of substrates by determining seven atomic structures of substrate-engaged 26S proteasome simultaneously.<ref name="Dong" />

[[File:3 conformational states of 26S proteasome.jpg|thumb|300px|Three distinct conformational states of the 26S proteasome.<ref name=Unverdorben/> The conformations are hypothesized to be responsible for recruitment of the substrate, its irreversible commitment, and finally processing and translocation into the core particle, where degradation occurs.]]