5LN3

The human 26S Proteasome at 6.8 Ang.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 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 Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.

Wang, X.Cimermancic, P.Yu, C.Schweitzer, A.Chopra, N.Engel, J.L.Greenberg, C.Huszagh, A.S.Beck, F.Sakata, E.Yang, Y.Novitsky, E.J.Leitner, A.Nanni, P.Kahraman, A.Guo, X.Dixon, J.E.Rychnovsky, S.D.Aebersold, R.Baumeister, W.Sali, A.Huang, L.

(2017) Mol Cell Proteomics 16: 840-854

  • DOI: 10.1074/mcp.M116.065326
  • Primary Citation of Related Structures:  
    5LN3

  • PubMed Abstract: 
  • The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms ...

    The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells. To facilitate the identification of cross-linked peptides, we have previously developed a robust amine reactive sulfoxide-containing MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). To better understand the structure and regulation of the human 26S proteasome, we have established new DSSO-based in vivo and in vitro XL-MS workflows by coupling with HB-tag based affinity purification to comprehensively examine protein-protein interactions within the 26S proteasome. In total, we have identified 447 unique lysine-to-lysine linkages delineating 67 interprotein and 26 intraprotein interactions, representing the largest cross-link dataset for proteasome complexes. In combination with EM maps and computational modeling, the architecture of the 26S proteasome was determined to infer its structural dynamics. In particular, three proteasome subunits Rpn1, Rpn6, and Rpt6 displayed multiple conformations that have not been previously reported. Additionally, cross-links between proteasome subunits and 15 proteasome interacting proteins including 9 known and 6 novel ones have been determined to demonstrate their physical interactions at the amino acid level. Our results have provided new insights on the dynamics of the 26S human proteasome and the methodologies presented here can be applied to study other protein complexes.


    Organizational Affiliation

    From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697; lanhuang@uci.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2A [auth Z]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6B [auth 1]239Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7C [auth 2]277Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3D [auth 3]205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2E [auth 4]201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5F [auth 5]263Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1G [auth 6]241Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4H [auth 7]264Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6I [auth A]246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2J [auth B]234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4K [auth C]261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7L [auth D]248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5M [auth E]241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1N [auth F]263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 15
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Proteasome subunit alpha type-3O [auth G]255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 7P [auth H]433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 4Q [auth I]440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 18
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26S protease regulatory subunit 8R [auth J]406Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 19
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26S protease regulatory subunit 6BS [auth K]418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 20
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26S protease regulatory subunit 10BT [auth L]389Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 21
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26S protease regulatory subunit 6AU [auth M]439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 22
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26S proteasome non-ATPase regulatory subunit 1V [auth N]953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 23
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26S proteasome non-ATPase regulatory subunit 13W [auth O]376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 24
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26S proteasome non-ATPase regulatory subunit 12X [auth P]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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Entity ID: 25
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26S proteasome non-ATPase regulatory subunit 11Y [auth Q]422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 26
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26S proteasome non-ATPase regulatory subunit 6Z [auth R]389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 27
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26S proteasome non-ATPase regulatory subunit 3AA [auth S]534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8BA [auth T]350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 29
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26S proteasome non-ATPase regulatory subunit 7CA [auth U]324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 30
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26S proteasome non-ATPase regulatory subunit 14DA [auth V]310Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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Entity ID: 31
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26S proteasome non-ATPase regulatory subunit 4EA [auth W]377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 32
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26S proteasome complex subunit DSS1FA [auth Y]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-05-24
    Changes: Database references