5MPE

26S proteasome in presence of ATP (s2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the functional cycle of the ATPase module of the 26S proteasome.

Wehmer, M.Rudack, T.Beck, F.Aufderheide, A.Pfeifer, G.Plitzko, J.M.Forster, F.Schulten, K.Baumeister, W.Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

  • DOI: https://doi.org/10.1073/pnas.1621129114
  • Primary Citation of Related Structures:  
    5MP9, 5MPA, 5MPB, 5MPC, 5MPD, 5MPE

  • PubMed Abstract: 

    In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis.


  • Organizational Affiliation

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN10A [auth W]268Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38886 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38886 
Go to UniProtKB:  P38886
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38886
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11B [auth V]306Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43588 
Go to UniProtKB:  P43588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43588
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12C [auth T]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32496 
Go to UniProtKB:  P32496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32496
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN13D [auth X]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for O13563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O13563 
Go to UniProtKB:  O13563
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13563
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1E [auth Y]89Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O94742 
Go to UniProtKB:  O94742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1F [auth Z]993Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38764 
Go to UniProtKB:  P38764
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38764
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN2G [auth N]945Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32565 
Go to UniProtKB:  P32565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32565
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN3H [auth S]523Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40016 
Go to UniProtKB:  P40016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40016
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN5I [auth P]445Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12250 
Go to UniProtKB:  Q12250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12250
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN6J [auth Q]434Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12377 
Go to UniProtKB:  Q12377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12377
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN7K [auth R]429Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06103 
Go to UniProtKB:  Q06103
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06103
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8L [auth U]338Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08723 
Go to UniProtKB:  Q08723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08723
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN9M [auth O]393Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q04062 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04062 
Go to UniProtKB:  Q04062
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04062
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB-1035
National Science FoundationUnited StatesPHY1430124
National Institutes of HealthUnited States9P41GM104601

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references