6EF0

Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.43 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 ...

    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-1A238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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: PRE8PRS4YML092C
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3C244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4D242Saccharomyces 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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E249Saccharomyces 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: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6F234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7G246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homologH257Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homologI271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homologJ276Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homologK272Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome subunit RPT4L273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AM258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
model substrate polypeptides12Homo sapiensMutation(s): 0 
Find proteins for P07818 (Arbacia punctulata)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
I, J, K
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H, L, M
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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 

  • 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: 2019-12-18
    Changes: Author supporting evidence, Other