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, 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1A [auth 1]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38624 
Go to UniProtKB:  P38624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38624
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2B [auth 2]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25043 
Go to UniProtKB:  P25043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25043
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3C [auth 3]205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25451 
Go to UniProtKB:  P25451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25451
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4D [auth 4]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22141 
Go to UniProtKB:  P22141
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22141
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5E [auth 5]287Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30656 
Go to UniProtKB:  P30656
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30656
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6F [auth 6]241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23724 
Go to UniProtKB:  P23724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23724
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7G [auth 7]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30657 
Go to UniProtKB:  P30657
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30657
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1H [auth A]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21243 
Go to UniProtKB:  P21243
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21243
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2I [auth B]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23639 
Go to UniProtKB:  P23639
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23639
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3J [auth C]258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23638 
Go to UniProtKB:  P23638
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23638
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4K [auth D]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40303 
Go to UniProtKB:  P40303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40303
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5L [auth E]260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32379 
Go to UniProtKB:  P32379
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32379
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6M [auth F]234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40302 
Go to UniProtKB:  P40302
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40302
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7N [auth G]288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21242 
Go to UniProtKB:  P21242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21242
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homologO [auth H]467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
UniProt
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33299 
Go to UniProtKB:  P33299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33299
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homologP [auth I]437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
UniProt
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40327 
Go to UniProtKB:  P40327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40327
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homologQ [auth J]405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
UniProt
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01939 
Go to UniProtKB:  Q01939
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01939
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homologR [auth K]428Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
UniProt
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33298 
Go to UniProtKB:  P33298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33298
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome subunit RPT4S [auth L]437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
UniProt
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53549 
Go to UniProtKB:  P53549
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53549
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AT [auth M]434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
UniProt
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33297 
Go to UniProtKB:  P33297
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33297
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7U [auth n]15Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PSB7PRE4YFR050C
EC: 3.4.25.1
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30657 
Go to UniProtKB:  P30657
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30657
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11V [auth r]306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN11MPR1YFR004W
EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43588 
Go to UniProtKB:  P43588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43588
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Model substrate polypeptideW [auth s]38Homo sapiensMutation(s): 0 
UniProt
Find proteins for P07818 (Arbacia punctulata)
Explore P07818 
Go to UniProtKB:  P07818
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07818
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40X [auth u]128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CH08 
Go to UniProtKB:  P0CH08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CH08
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth J],
DA [auth M],
Y [auth H],
Z [auth I]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth K],
CA [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
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