5MPD

26S proteasome in presence of ATP (s1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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

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: 10.1073/pnas.1621129114
  • Primary Citation of Related Structures:  

  • 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 particle ...

    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.,Beckman Institute, Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Urbana, IL 61801.,Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de sakata@biochem.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN10
W
268Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN10 (MCB1, SUN1)
Find proteins for P38886 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38886
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase RPN11
V
306Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN11 (MPR1)
EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43588
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN12
T
274Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN12 (NIN1)
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32496
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN13
X
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN13 (DAQ1)
Find proteins for O13563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13563
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit SEM1
Y
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEM1 (DSH1)
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SEM1
Go to UniProtKB:  O94742
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN1
Z
993Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN1 (HRD2, NAS1, RPD1)
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPN1
Go to UniProtKB:  P38764
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN2
N
945Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN2 (SEN3)
Find proteins for P32565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPN2
Go to UniProtKB:  P32565
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN3
S
523Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN3 (SUN2)
Find proteins for P40016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40016
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN5
P
445Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN5 (NAS5)
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12250
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN6
Q
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN6 (NAS4)
Find proteins for Q12377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12377
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN7
R
429Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN7
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06103
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN8
U
338Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN8
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08723
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN9
O
393Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN9 (NAS7)
Find proteins for Q04062 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04062
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Data collection