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 esse ...

    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 2Z908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
Find proteins for Q13200 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-61239Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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PHAROS  P28072
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-72277Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
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PHAROS  Q99436
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-33205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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PHAROS  P49720
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-24201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-55263Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-16241Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-47264Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
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PHAROS  P28070
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6A246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 7H433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
Find proteins for P35998 (Homo sapiens)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 4I440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 8J406Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
Find proteins for P62195 (Homo sapiens)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BK418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BL389Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
Find proteins for P62333 (Homo sapiens)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AM439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
Find proteins for P17980 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1N953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13O376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12P456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11Q422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6R389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3S534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8T350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7U324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14V310Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4W377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1Y70Homo 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 

  • 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