6MSJ

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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
Find proteins for Q99460 (Homo sapiens)
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GTEx  ENSG00000173692
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3V533Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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GTEx  ENSG00000108344
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12W456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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GTEx  ENSG00000197170
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11X422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
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GTEx  ENSG00000108671
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6Y389Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
Find proteins for Q15008 (Homo sapiens)
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GTEx  ENSG00000163636
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Entity ID: 6
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26S proteasome non-ATPase regulatory subunit 7Z324Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
Find proteins for P51665 (Homo sapiens)
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GTEx  ENSG00000103035
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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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GTEx  ENSG00000185627
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4b377Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens)
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GTEx  ENSG00000159352
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14c309Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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GTEx  ENSG00000115233
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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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GTEx  ENSG00000099341
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Entity ID: 11
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26S proteasome complex subunit SEM1e70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
Find proteins for P60896 (Homo sapiens)
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GTEx  ENSG00000127922
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 2f892Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
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GTEx  ENSG00000175166
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Entity ID: 13
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26S proteasome regulatory subunit 7A433Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
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GTEx  ENSG00000161057
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Entity ID: 14
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Rpt2, NP_002793.2 (26SHA chain B)B440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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GTEx  ENSG00000100764
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Entity ID: 15
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26S proteasome regulatory subunit 8C398Homo sapiensMutation(s): 0 
Gene Names: PSMC5, SUG1
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GTEx  ENSG00000087191
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Entity ID: 16
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26S proteasome regulatory subunit 6BD418Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
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GTEx  ENSG00000013275
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Entity ID: 17
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26S proteasome regulatory subunit 10BE403Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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Entity ID: 18
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26S proteasome regulatory subunit 6AF439Homo sapiensMutation(s): 0 
Gene Names: PSMC3, TBP1
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GTEx  ENSG00000165916
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Entity ID: 19
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substratev36Saccharomyces cerevisiae RM11-1aMutation(s): 0 
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Entity ID: 20
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Proteasome subunit alpha type-6G245Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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GTEx  ENSG00000100902
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Entity ID: 21
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Proteasome subunit alpha type-2H, h233Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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GTEx  ENSG00000106588
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Entity ID: 22
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Proteasome subunit alpha type-4I, i260Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
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GTEx  ENSG00000041357
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Entity ID: 23
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Proteasome subunit alpha type-7J, j247Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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GTEx  ENSG00000101182
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Entity ID: 24
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Proteasome subunit alpha type-5K, k240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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GTEx  ENSG00000143106
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1L, l268Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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GTEx  ENSG00000129084
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Entity ID: 26
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Proteasome subunit alpha type-3M, m254Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
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GTEx  ENSG00000100567
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Entity ID: 27
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Proteasome subunit beta type-6N, n238Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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GTEx  ENSG00000142507
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Entity ID: 28
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Proteasome subunit beta type-7O, o276Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
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GTEx  ENSG00000136930
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Entity ID: 29
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Proteasome subunit beta type-3P, p204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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GTEx  ENSG00000277791
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Entity ID: 30
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Proteasome subunit beta type-2Q, q201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx  ENSG00000126067
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Entity ID: 31
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Proteasome subunit beta type-5R, r262Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
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GTEx  ENSG00000100804
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Entity ID: 32
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Proteasome subunit beta type-1S, s240Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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GTEx  ENSG00000008018
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Entity ID: 33
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Proteasome subunit beta type-4T, t263Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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GTEx  ENSG00000159377
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6g240Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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GTEx  ENSG00000100902
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
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A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
Download CCD File 
E
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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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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