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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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. 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

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
UniProt
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UniProt GroupP21243
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
UniProt
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UniProt GroupP23639
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homolog262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homolog271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homolog273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homolog276Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome subunit RPT4271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
model substrate polypeptideN [auth s]15Homo sapiensMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11-2580

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
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Refinement description