5WVK

Yeast proteasome-ADP-AlFx


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx

Ding, Z.Fu, Z.Xu, C.Wang, Y.Wang, Y.Li, J.Kong, L.Chen, J.Li, N.Zhang, R.Cong, Y.

(2017) Cell Res. 27: 373-385

  • DOI: 10.1038/cr.2017.12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S protea ...

    The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.


    Organizational Affiliation

    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, 333 Haike Road, Shanghai 201203, 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 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))
Go to UniProtKB:  P53549
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))
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: 4.2 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-25 
  • Released Date: 2017-03-22 
  • Deposition Author(s): Ding, Z., Cong, Y.

Funding OrganizationLocationGrant Number
CASChinaXDB08030201
National Natural Science Foundation of ChinaChina31270771
National Natural Science Foundation of ChinaChina31222016
National Basic Research Program of ChinaChina2013CB910401
CASChinaKFJ-EW-STS-098
CASChinaCAS-SSRC-YH-2015-01

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release