5WVK

Yeast proteasome-ADP-AlFx

  • Classification: HYDROLASE
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2016-12-25 Released: 2017-03-22 
  • Deposition Author(s): Ding, Z., Cong, Y.
  • Funding Organization(s): CAS, National Natural Science Foundation of China, National Basic Research Program of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/cr.2017.12
  • Primary Citation of Related Structures:  
    5WVI, 5WVK

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1A [auth 1],
H [auth b]
215Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2B [auth 2],
I [auth i]
261Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3C [auth 3],
J [auth h]
205Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4D [auth 4],
K [auth g]
198Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5E [auth 5],
L [auth f]
287Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6F [auth 6],
M [auth e]
241Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7G [auth 7],
N [auth a]
266Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1O [auth A],
V [auth c]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2P [auth B],
W [auth j]
250Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3Q [auth C],
X [auth d]
258Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4R [auth D],
Y [auth n]
254Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5S [auth E],
Z [auth m]
260Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6AA [auth l],
T [auth F]
234Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7BA [auth k],
U [auth G]
288Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7 homologCA [auth H]467Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4 homologDA [auth I]437Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8 homologEA [auth J]405Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6B homologFA [auth K]428Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease subunit RPT4GA [auth L]437Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AHA [auth M]434Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN2IA [auth N]945Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN9JA [auth O]393Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN5KA [auth P]445Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN6LA [auth Q]434Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN7MA [auth R]429Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN3NA [auth S]523Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12OA [auth T]274Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8PA [auth U]338Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11QA [auth V]306Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.19.12
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN10RA [auth W]268Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN13SA [auth X]156Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1TA [auth Y]89Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1UA [auth Z]993Saccharomyces cerevisiae S288CMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Other
  • Version 1.2: 2019-10-23
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references