7QO3

Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Allosteric control of Ubp6 and the proteasome via a bidirectional switch.

Hung, K.Y.S.Klumpe, S.Eisele, M.R.Elsasser, S.Tian, G.Sun, S.Moroco, J.A.Cheng, T.C.Joshi, T.Seibel, T.Van Dalen, D.Feng, X.H.Lu, Y.Ovaa, H.Engen, J.R.Lee, B.H.Rudack, T.Sakata, E.Finley, D.

(2022) Nat Commun 13: 838-838

  • DOI: https://doi.org/10.1038/s41467-022-28186-y
  • Primary Citation of Related Structures:  
    7QO3, 7QO5, 7QO6

  • PubMed Abstract: 

    The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1A [auth a],
O [auth A]
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B [auth b],
P [auth B]
250Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3C [auth c],
Q [auth C]
258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4D [auth d],
R [auth D]
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E [auth e],
S [auth E]
260Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6F [auth f],
T [auth F]
234Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7G [auth g],
U [auth G]
288Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1H [auth h],
V [auth 1]
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2I [auth i],
W [auth 2]
261Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J [auth j],
X [auth 3]
205Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4K [auth k],
Y [auth 4]
198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L [auth l],
Z [auth 5]
287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6AA [auth 6],
M [auth m]
241Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7BA [auth 7],
N [auth n]
266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN10CA [auth W]268Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11DA [auth V]306Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.19.12
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12EA [auth T]274Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN13FA [auth X]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1GA [auth Y]89Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1HA [auth Z]993Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN2IA [auth N]945Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN3JA [auth S]523Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN5KA [auth P]445Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN6LA [auth Q]434Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN7MA [auth R]429Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8NA [auth U]338Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN9OA [auth O]393Saccharomyces cerevisiaeMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)EXC 2067/1- 390729940
German Research Foundation (DFG)SFB1035/Project A01
German Research Foundation (DFG)CRC889/Project A11
Other governmentMarie Curie Career Integration grant (PCIG14-GA-2013-631577)
Other governmentUnited StatesNational Institutes of Health R01 GM043601

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection