6MSG

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.

Dong, Y.Zhang, S.Wu, Z.Li, X.Wang, W.L.Zhu, Y.Stoilova-McPhie, S.Lu, Y.Finley, D.Mao, Y.

(2019) Nature 565: 49-55

  • DOI: 10.1038/s41586-018-0736-4
  • Primary Citation of Related Structures:  
    6MSE, 6MSD, 6MSG, 6MSH, 6MSK, 6MSJ, 6MSB

  • PubMed Abstract: 
  • The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven con ...

    The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.


    Organizational Affiliation

    Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, China. youdong_mao@dfci.harvard.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1U953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 2
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26S proteasome non-ATPase regulatory subunit 3V533Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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Entity ID: 3
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26S proteasome non-ATPase regulatory subunit 12W456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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Entity ID: 4
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26S proteasome non-ATPase regulatory subunit 11X422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
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26S proteasome non-ATPase regulatory subunit 6Y389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 7
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26S proteasome non-ATPase regulatory subunit 13a376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4b377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14c309Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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Entity ID: 10
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26S proteasome non-ATPase regulatory subunit 8d349Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
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26S proteasome complex subunit SEM1e70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 2f892Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Entity ID: 13
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26S proteasome regulatory subunit 7A433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 14
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26S proteasome regulatory subunit 4B440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 15
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26S proteasome regulatory subunit 8C398Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 16
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26S proteasome regulatory subunit 6BD418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 17
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26S proteasome regulatory subunit 10BE403Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 18
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26S proteasome regulatory subunit 6AF439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 19
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Ubiquitinu76Homo sapiensMutation(s): 0 
Gene Names: UBB
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
substratev24Saccharomyces cerevisiae RM11-1aMutation(s): 0 
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Entity ID: 21
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Proteasome subunit alpha type-6Gg245Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 22
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Proteasome subunit alpha type-2Hh233Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4Ii260Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7Jj247Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5Kk240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1Ll268Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7Oo276Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3Pp204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 31
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Proteasome subunit beta type-2Qq201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 32
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Proteasome subunit beta type-5Rr262Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 33
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Proteasome subunit beta type-1Ss240Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 34
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Proteasome subunit beta type-4Tt263Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 27
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Proteasome subunit alpha type-3Mm254Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 28
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Proteasome subunit beta type-6Nn238Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 6
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26S proteasome non-ATPase regulatory subunit 7Z324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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C, D, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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A, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-16 
  • Released Date: 2018-11-21 
  • Deposition Author(s): Mao, Y.D.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China11774012
National Natural Science Foundation of China (NSFC)China91530321
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM43601

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence