6WJD

SA-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: 2020-04-13 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: 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

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: 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 ...

    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

    Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: kylie.walters@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1 U953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3 V534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12 W456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11 X422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6 Y389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
Find proteins for Q15008 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7 Z324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13 a376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4 b377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14 c309Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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Entity ID: 10
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26S proteasome non-ATPase regulatory subunit 8 d349Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1 e70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 2 f908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 A433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 B440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 C398Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B D418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10B E403Homo sapiensMutation(s): 0 
Gene Names: PSMC6
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Entity ID: 18
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26S proteasome regulatory subunit 6A F439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin u76Homo sapiensMutation(s): 0 
Gene Names: UBC
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 Gg245Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 Hh233Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 Ii260Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 23
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Proteasome subunit alpha type-7 Jj247Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 Kk240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 Ll268Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 Mm254Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6 Nn238Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7 Oo276Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 Pp204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2 Qq201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 31
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Proteasome subunit beta type-5 Rr262Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 32
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Proteasome subunit beta type-1 Ss240Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 33
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Proteasome subunit beta type-4 Tt263Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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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


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