6J30

yeast proteasome in Ub-engaged state (C2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 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 Snapshots of 26S Proteasome Reveal Tetraubiquitin-Induced Conformations.

Ding, Z.Xu, C.Sahu, I.Wang, Y.Fu, Z.Huang, M.Wong, C.C.L.Glickman, M.H.Cong, Y.

(2019) Mol. Cell 73: 1150

  • DOI: 10.1016/j.molcel.2019.01.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how proteasome responds to ubiquitin signal, we resolved an ...

    The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how proteasome responds to ubiquitin signal, we resolved an ensemble of cryo-EM structures of proteasome in the presence of K48-Ub 4 , with three of them resolved at near-atomic resolution. We identified a conformation with stabilized ubiquitin receptors and a previously unreported orientation of the lid, assigned as a Ub-accepted state C1-b. We determined another structure C3-b with localized K48-Ub 4 to the toroid region of Rpn1, assigned as a substrate-processing state. Our structures indicate that tetraUb induced conformational changes in proteasome could initiate substrate degradation. We also propose a CP gate-opening mechanism involving the propagation of the motion of the lid to the gate through the Rpn6-α2 interaction. Our results enabled us to put forward a model of a functional cycle for proteasomes induced by tetraUb and nucleotide.


    Organizational Affiliation

    Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China. Electronic address: cong@sibcb.ac.cn.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
1, b
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 subunit beta type-2
2, i
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 subunit beta type-3
3, h
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 subunit beta type-4
4, g
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 subunit beta type-5
5, f
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 subunit beta type-6
6, e
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 subunit beta type-7
7, a
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 subunit alpha type-1
A, c
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 subunit alpha type-2
B, j
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 subunit alpha type-3
C, d
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 subunit alpha type-4
D, n
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 subunit alpha type-5
E, m
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 subunit alpha type-6
F, l
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))
Go to UniProtKB:  P40302
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
G, k
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 proteasome 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 proteasome 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 proteasome 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 proteasome 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 proteasome 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))
Go to UniProtKB:  P53549
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S proteasome 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))
Go to UniProtKB:  P33297
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
Go to UniProtKB:  P32565
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))
Go to UniProtKB:  Q12377
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))
Go to UniProtKB:  P40016
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))
Go to UniProtKB:  P32496
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))
Go to UniProtKB:  Q08723
Entity ID: 29
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: 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))
Go to UniProtKB:  P38886
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))
Go to Gene View: SEM1
Go to UniProtKB:  O94742
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: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-01-03 
  • Released Date: 2019-03-20 
  • Deposition Author(s): Cong, Y.

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references