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: https://doi.org/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. 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

    §Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94143.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2A [auth Z]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6B [auth 1]239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7C [auth 2]277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3D [auth 3]205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2E [auth 4]201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5F [auth 5]263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1G [auth 6]241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4H [auth 7]264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6I [auth A]246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2J [auth B]234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4K [auth C]261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7L [auth D]248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5M [auth E]241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1N [auth F]263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3O [auth G]255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7P [auth H]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4Q [auth I]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8R [auth J]406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BS [auth K]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BT [auth L]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AU [auth M]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1V [auth N]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13W [auth O]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12X [auth P]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11Y [auth Q]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6Z [auth R]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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26S proteasome non-ATPase regulatory subunit 3AA [auth S]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8BA [auth T]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7CA [auth U]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14DA [auth V]310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4EA [auth W]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1FA [auth Y]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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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