6WJN

SD-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A

  • Classification: HYDROLASE/PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-04-14 Released: 2020-08-05 
  • Deposition Author(s): Chen, X., Walters, K.J.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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

Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome.

Chen, X.Dorris, Z.Shi, D.Huang, R.K.Khant, H.Fox, T.de Val, N.Williams, D.Zhang, P.Walters, K.J.

(2020) Structure 28: 1206-1217.e4

  • DOI: https://doi.org/10.1016/j.str.2020.07.011
  • Primary Citation of Related Structures:  
    6WJD, 6WJN

  • PubMed Abstract: 

    The 26S proteasome is specialized for regulated protein degradation and formed by a dynamic regulatory particle (RP) that caps a hollow cylindrical core particle (CP) where substrates are proteolyzed. Its diverse substrates unify as proteasome targets by ubiquitination. We used cryogenic electron microscopy (cryo-EM) to study how human 26S proteasome interacts with M1-linked hexaubiquitin (M1-Ub 6 ) unanchored to a substrate and E3 ubiquitin ligase E6AP/UBE3A. Proteasome structures are available with model substrates extending through the RP ATPase ring and substrate-conjugated K63-linked ubiquitin chains present at inhibited deubiquitinating enzyme hRpn11 and the nearby ATPase hRpt4/hRpt5 coiled coil. In this study, we find M1-Ub 6 at the hRpn11 site despite the absence of conjugated substrate, indicating that ubiquitin binding at this location does not require substrate interaction with the RP. Moreover, unanchored M1-Ub 6 binds to this hRpn11 site of the proteasome with the CP gating residues in both the closed and opened conformational states.


  • Organizational Affiliation

    John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe, AZ 85287, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth U]911Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth V]480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12C [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth X]380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13G [auth a]373Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4H [auth b]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8J [auth d]257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1K [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6L [auth G],
Z [auth g]
240Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2AA [auth h],
M [auth H]
232Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4BA [auth i],
N [auth I]
250Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7CA [auth j],
O [auth J]
243Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5DA [auth k],
P [auth K]
234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1EA [auth l],
Q [auth L]
238Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3FA [auth m],
R [auth M]
245Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6GA [auth n],
S [auth N]
191Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7HA [auth o],
T [auth O]
220Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3IA [auth p],
U [auth P]
204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2JA [auth q],
V [auth Q]
199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5KA [auth r],
W [auth R]
201Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1LA [auth s],
X [auth S]
213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4MA [auth t],
Y [auth T]
215Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7NA [auth A]399Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4OA [auth B]389Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8PA [auth C]392Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BQA [auth D]380Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BRA [auth E]375Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6ASA [auth F]396Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2TA [auth f]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1 ZIA BC011490
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCCR FLEX program
National Science Foundation (NSF, United States)United States1531991

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references