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 1.2 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:  

  • PubMed Abstract: 
  • The 26 <i>S </i> 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.,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. glander@scripps.edu a.martin@berkeley.edu.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA. glander@scripps.edu a.martin@berkeley.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
1
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
2
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
3
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
4
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
5
287Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
6
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
7
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
A
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
B
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
C
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
D
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
E
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
F
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
G
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 7 homolog
H
467Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT1 (CIM5, YTA3)
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33299
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 4 homolog
I
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT2 (YHS4, YTA5)
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40327
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 8 homolog
J
405Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT6 (CIM3, CRL3, SUG1, TBPY, TBY1)
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01939
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6B homolog
K
428Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT3 (YNT1, YTA2)
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33298
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S proteasome subunit RPT4
L
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT4 (CRL13, PCS1, SUG2)
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53549
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6A
M
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPT5 (YTA1)
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33297
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
n
15Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase RPN11
r
306Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN11 (MPR1)
EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43588
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Model substrate polypeptide
s
38Arbacia punctulataMutation(s): 0 
Find proteins for P07818 (Arbacia punctulata)
Go to UniProtKB:  P07818
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
u
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download SDF File 
Download CCD File 
K, 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 or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM094497
National Institutes of Health/National Institute of General Medical SciencesUnited StatesDP2-EB020402

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-12-12
    Type: Data collection, Database references