3JCK

Structure of the yeast 26S proteasome lid sub-complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history. 


Literature

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.

Dambacher, C.M., Worden, E.J., Herzik, M.A., Martin, A., Lander, G.C.

(2016) Elife 5: e13027-e13027

  • DOI: 10.7554/eLife.13027
  • Primary Citation of Related Structures:  
    3JCK

  • PubMed Abstract: 

    • The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex ...

    The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex. Prior to the lid's incorporation into the proteasome, Rpn11 deubiquitinase activity is inhibited to prevent unwarranted deubiquitination of polyubiquitinated proteins. Here we present the atomic model of the isolated lid sub-complex, as determined by cryo-electron microscopy at 3.5 Å resolution, revealing how Rpn11 is inhibited through its interaction with a neighboring lid subunit, Rpn5. Through mutagenesis of specific residues, we describe the network of interactions that are required to stabilize this inhibited state. These results provide significant insight into the intricate mechanisms of proteasome assembly, outlining the substantial conformational rearrangements that occur during incorporation of the lid into the 26S holoenzyme, which ultimately activates the deubiquitinase for substrate degradation.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN3A438Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN3, SUN2, YER021W
UniProt
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UniProt GroupP40016
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN5B445Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN5, NAS5, YDL147W, D1572
UniProt
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN6C434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN6, NAS4, YDL097C, D2381
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN7D429Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN7, YPR108W, P8283.8
UniProt
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8E338Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN8, YOR261C, O5360
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN9F393Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN9, NAS7, YDR427W, D9461.14
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11G306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN11, MPR1, YFR004W
EC: 3.4.19.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12H274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN12, NIN1, YFR052W
UniProt
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
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26S proteasome complex subunit SEM1I89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEM1, DSH1, YDR363W-A
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth G]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection