6EF1

Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.73 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, 6EF1, 6EF2, 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 alpha type-1A239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
EC: 3.4.25.1
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3C238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4D234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6F233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7G243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homologH262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1, CIM5, YTA3, YKL145W
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homologI271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2, YHS4, YTA5, YDL007W, D2920
UniProt
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homologJ273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6, CIM3, CRL3, SUG1, TBPY, TBY1, YGL048C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homologK276Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3, YNT1, YTA2, YDR394W, D9509.14
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome subunit RPT4L271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4, CRL13, PCS1, SUG2, YOR259C
UniProt
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AM262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5, YTA1, YOR117W, O3258, YOR3258W
UniProt
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
model substrate polypeptideN [auth s]15Homo sapiensMutation(s): 0 
UniProt
Find proteins for P07818 (Arbacia punctulata)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

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