3JCP

Structure of yeast 26S proteasome in M2 state derived from Titan dataset


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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

Structure of an endogenous yeast 26S proteasome reveals two major conformational states.

Luan, B.Huang, X.L.Wu, J.P.Shi, Y.G.Wang, F.

(2016) Proc Natl Acad Sci U S A 113: 2642-2647

  • DOI: 10.1073/pnas.1601561113
  • Primary Citation of Related Structures:  
    3JCO, 3JCP

  • PubMed Abstract: 
  • The eukaryotic proteasome mediates degradation of polyubiquitinated proteins. Here we report the single-particle cryoelectron microscopy (cryo-EM) structures of the endogenous 26S proteasome from Saccharomyces cerevisiae at 4.6- to 6.3-Å resolution. The fine features of the cryo-EM maps allow modeling of 18 subunits in the regulatory particle and 28 in the core particle ...

    The eukaryotic proteasome mediates degradation of polyubiquitinated proteins. Here we report the single-particle cryoelectron microscopy (cryo-EM) structures of the endogenous 26S proteasome from Saccharomyces cerevisiae at 4.6- to 6.3-Å resolution. The fine features of the cryo-EM maps allow modeling of 18 subunits in the regulatory particle and 28 in the core particle. The proteasome exhibits two distinct conformational states, designated M1 and M2, which correspond to those reported previously for the proteasome purified in the presence of ATP-γS and ATP, respectively. These conformations also correspond to those of the proteasome in the presence and absence of exogenous substrate. Structure-guided biochemical analysis reveals enhanced deubiquitylating enzyme activity of Rpn11 upon assembly of the lid. Our structures serve as a molecular basis for mechanistic understanding of proteasome function.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; shi-lab@tsinghua.edu.cn wfeng@tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6A [auth 1], H [auth 8]241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7B [auth 2], I [auth 9]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1C [auth 3], QA [auth h]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2D [auth 4], RA [auth i]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3E [auth 5], SA [auth j]205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4F [auth 6], TA [auth k]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5G [auth 7], UA [auth l]287Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1J [auth A], JA [auth a]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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Entity ID: 9
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Proteasome subunit alpha type-2K [auth B], KA [auth b]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
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Entity ID: 10
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Proteasome subunit alpha type-3L [auth C], LA [auth c]258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
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Entity ID: 11
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Proteasome subunit alpha type-4M [auth D], MA [auth d]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
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Entity ID: 12
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Proteasome subunit alpha type-5N [auth E], NA [auth e]260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
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Entity ID: 13
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Proteasome subunit alpha type-6O [auth F], OA [auth f]234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7P [auth G], PA [auth g]288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 7 homologQ [auth H]467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
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Entity ID: 16
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26S protease regulatory subunit 4 homologR [auth I]437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 8 homologS [auth J]405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6B homologT [auth K]428Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
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Entity ID: 19
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26S protease subunit RPT4U [auth L]437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
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Entity ID: 20
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26S protease regulatory subunit 6AV [auth M]434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
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Entity ID: 21
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26S proteasome regulatory subunit RPN2W [auth N]945Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN2SEN3YIL075C
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Entity ID: 22
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26S proteasome regulatory subunit RPN9X [auth O]393Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN9NAS7YDR427WD9461.14
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Entity ID: 23
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26S proteasome regulatory subunit RPN5Y [auth P]445Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN5NAS5YDL147WD1572
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Entity ID: 24
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26S proteasome regulatory subunit RPN6Z [auth Q]434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN6NAS4YDL097CD2381
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Entity ID: 25
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26S proteasome regulatory subunit RPN7AA [auth R]429Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN7YPR108WP8283.8
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Entity ID: 26
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26S proteasome regulatory subunit RPN3BA [auth S]523Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN3SUN2YER021W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12CA [auth T]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN12NIN1YFR052W
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Entity ID: 28
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26S proteasome regulatory subunit RPN8DA [auth U]338Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN8YOR261CO5360
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Entity ID: 29
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Ubiquitin carboxyl-terminal hydrolase RPN11EA [auth V]306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN11MPR1YFR004W
EC: 3.4.19.12
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Entity ID: 30
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26S proteasome regulatory subunit RPN10FA [auth W]268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN10MCB1SUN1YHR200W
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Entity ID: 31
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26S proteasome regulatory subunit RPN13GA [auth X]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN13DAQ1YLR421C
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Entity ID: 32
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26S proteasome complex subunit SEM1HA [auth Y]89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEM1DSH1YDR363W-A
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Entity ID: 33
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26S proteasome regulatory subunit RPN1IA [auth Z]993Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN1HRD2NAS1RPD1YHR027C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Other
  • Version 1.2: 2019-12-18
    Changes: Data collection, Database references