Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A1B1C1D1E1F1G1H1I1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 361.33 kDa 
• Atom Count: 22457 
• Modelled Residue Count: 2777 
• Deposited Residue Count: 3146 
• Unique protein chains: 9

3JCK

Structure of the yeast 26S proteasome lid sub-complex

• DOI: 10.2210/pdb3JCK/pdb
• EMDataResource: EMD-6479

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-20 Released: 2016-01-20 
• Deposition Author(s): Herzik Jr., M.A., Dambacher, C.M., Worden, E.J., Martin, A., Lander, G.C.

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Experimental Data Snapshot

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

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

• PubMed: 26744777 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN3	A	438	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN3, SUN2, YER021W
Find proteins for P40016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40016  Go to UniProtKB:  P40016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN5	B	445	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN5, NAS5, YDL147W, D1572
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12250  Go to UniProtKB:  Q12250

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN6	C	434	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN6, NAS4, YDL097C, D2381
Find proteins for Q12377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12377  Go to UniProtKB:  Q12377

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN7	D	429	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN7, YPR108W, P8283.8
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06103  Go to UniProtKB:  Q06103

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN8	E	338	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN8, YOR261C, O5360
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08723  Go to UniProtKB:  Q08723

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN9	F	393	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN9, NAS7, YDR427W, D9461.14
Find proteins for Q04062 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04062  Go to UniProtKB:  Q04062

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase RPN11	G	306	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN11, MPR1, YFR004W EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43588  Go to UniProtKB:  P43588

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN12	H	274	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN12, NIN1, YFR052W
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32496  Go to UniProtKB:  P32496

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	I	89	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SEM1, DSH1, YDR363W-A
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O94742  Go to UniProtKB:  O94742

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-20 
• Released Date: 2016-01-20 
Deposition Author(s): Herzik Jr., M.A., Dambacher, C.M., Worden, E.J., Martin, A., Lander, G.C.

Revision History  

• 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