4CR4

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.8 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

Deep Classification of a Large Cryo-Em Dataset Defines the Conformational Landscape of the 26S Proteasome.

Unverdorben, P., Beck, F., Sledz, P., Schweitzer, A., Pfeifer, G., Plitzko, J.M., Baumeister, W., Forster, F.

(2014) Proc.Natl.Acad.Sci.USA 111: 5544

  • DOI: 10.1073/pnas.1403409111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed underst ...

    The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.

    Organizational Affiliation: 

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




Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE3
1
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP1
2
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP3
3
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C11
4
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE2
5
287Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C5
6
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE4
7
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C7-ALPHA
A
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT Y7
B
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT Y13
C
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE6
D
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP2
E
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE5
F
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C1
G
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG
H
467Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT1 (CIM5, YTA3)
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33299
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOG
I
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT2 (YHS4, YTA5)
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40327
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOG
J
405Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT6 (CIM3, CRL3, SUG1, TBPY, TBY1)
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01939
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOG
K
428Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT3 (YNT1, YTA2)
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33298
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE SUBUNIT RPT4
L
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT4 (CRL13, PCS1, SUG2)
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 6A
M
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT5 (YTA1)
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
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
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Entity ID: 22
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
Entity ID: 23
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: 24
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))
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Entity ID: 25
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: 26
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))
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Entity ID: 27
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))
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Entity ID: 28
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))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT 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))
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Entity ID: 30
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))
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Entity ID: 31
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: 32
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))
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Entity ID: 33
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references
  • Version 1.2: 2014-04-30
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Data collection