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: 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 ...

    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-1239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2250Saccharomyces 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-3238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7243Saccharomyces 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 homolog262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1, CIM5, YTA3, YKL145W
UniProt
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Entity ID: 9
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26S proteasome regulatory subunit 4 homolog271Saccharomyces 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 homolog273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6, CIM3, CRL3, SUG1, TBPY, TBY1, YGL048C
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homolog276Saccharomyces 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 RPT4271Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4, CRL13, PCS1, SUG2, YOR259C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5, YTA1, YOR117W, O3258, YOR3258W
UniProt
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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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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
O [auth H],
P [auth I],
Q [auth J],
R [auth K]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
S [auth L],
T [auth M]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
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



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