7QYA

Proteasome-ZFAND5 Complex Z-B state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism for activation of the 26S proteasome by ZFAND5.

Lee, D.Zhu, Y.Colson, L.Wang, X.Chen, S.Tkacik, E.Huang, L.Ouyang, Q.Goldberg, A.L.Lu, Y.

(2023) Mol Cell 83: 2959-2975.e7

  • DOI: https://doi.org/10.1016/j.molcel.2023.07.023
  • Primary Citation of Related Structures:  
    7QXN, 7QXP, 7QXU, 7QXW, 7QXX, 7QY7, 7QYA, 7QYB

  • PubMed Abstract: 

    Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated proteins can increase, we studied mouse ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn-finger domain interacts with the Rpt5 ATPase and its C terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Upon proteasome binding, ZFAND5 widens the entrance of the substrate translocation channel, yet it associates only transiently with the proteasome. Dissociation of ZFAND5 then stimulates opening of the 20S proteasome gate. Using single-molecule microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13A [auth a]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4B [auth b]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14C [auth c]309Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8D [auth d]349Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1E [auth e]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2F [auth f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1G [auth U]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3H [auth V]533Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12I [auth W]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11J [auth X]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6K [auth Y]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7L [auth Z]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7M [auth A]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4N [auth B]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of 26S proteasome regulatory subunit 8O [auth C]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BP [auth D]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BQ [auth E]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AR [auth F]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6GA [auth g],
S [auth G]
245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100902 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2HA [auth h],
T [auth H]
233Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106588 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4IA [auth i],
U [auth I]
260Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000041357 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7JA [auth j],
V [auth J]
247Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101182 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5KA [auth k],
W [auth K]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143106 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Long of Proteasome subunit alpha type-1LA [auth l],
X [auth L]
268Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129084 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3MA [auth m],
Y [auth M]
254Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100567 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6NA [auth n],
Z [auth N]
238Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth O],
OA [auth o]
276Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3BA [auth P],
PA [auth p]
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2CA [auth Q],
QA [auth q]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5DA [auth R],
RA [auth r]
262Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1EA [auth S],
SA [auth s]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008018 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4FA [auth T],
TA [auth t]
263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159377 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-08 
  • Deposition Author(s): Zhu, Y., Lu, Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary