6EF3

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Substrate-engaged 26Sproteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation.

de la Pena, A.H.Goodall, E.A.Gates, S.N.Lander, G.C.Martin, A.

(2018) Science 362

  • DOI: 10.1126/science.aav0725
  • Primary Citation of Related Structures:  
    6EF0, 6EF2, 6EF1, 6EF3

  • PubMed Abstract: 
  • The 26 S proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the proteasome unfolds and translocates targeted protein substrates into the open gate of a proteolytic core while a proteasomal deubiquitinase concomitantly removes substrate-attached ubiquitin chains ...

    The 26 S proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the proteasome unfolds and translocates targeted protein substrates into the open gate of a proteolytic core while a proteasomal deubiquitinase concomitantly removes substrate-attached ubiquitin chains. However, the mechanisms by which ATP hydrolysis drives the conformational changes responsible for these processes have remained elusive. Here we present the cryo-electron microscopy structures of four distinct conformational states of the actively ATP-hydrolyzing, substrate-engaged 26 S proteasome. These structures reveal how mechanical substrate translocation accelerates deubiquitination and how ATP-binding, -hydrolysis, and phosphate-release events are coordinated within the AAA+ (ATPases associated with diverse cellular activities) motor to induce conformational changes and propel the substrate through the central pore.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1 1215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2 2261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 3205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4 4198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5 5287Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6 6241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7 7266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 A252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 B250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 C258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 D254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 E260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 F234Saccharomyces 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-7 G288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homolog H467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homolog I437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homolog J405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homolog K428Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome subunit RPT4 L437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A M434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7 n15Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PSB7PRE4YFR050C
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11 r306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN11MPR1YFR004W
EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Model substrate polypeptide s38Homo sapiensMutation(s): 0 
Find proteins for P07818 (Arbacia punctulata)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40 u128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM094497
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2-EB020402

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence