6MSB

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

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2018-10-16 Released: 2018-12-05 
  • Deposition Author(s): Mao, Y.D.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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:  
    6MSB, 6MSD, 6MSE, 6MSG, 6MSH, 6MSJ, 6MSK

  • 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 conformational states at 2 ...

    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 1A [auth U]953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 2
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26S proteasome non-ATPase regulatory subunit 3B [auth V]534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Entity ID: 3
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26S proteasome non-ATPase regulatory subunit 12C [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth X]422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 6
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26S proteasome non-ATPase regulatory subunit 7F [auth Z]324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 7
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26S proteasome non-ATPase regulatory subunit 13G [auth a]376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4H [auth b]377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14I [auth c]309Homo 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 8J [auth d]349Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
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26S proteasome complex subunit SEM1K [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 2L [auth f]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7M [auth A]433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 14
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26S proteasome regulatory subunit 4N [auth B]440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 15
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26S proteasome regulatory subunit 8O [auth C]398Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 16
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26S proteasome regulatory subunit 6BP [auth D]418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 17
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26S proteasome regulatory subunit 10BQ [auth E]403Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 18
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26S proteasome regulatory subunit 6AR [auth F]439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinS [auth u], T [auth w]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6U [auth G], IA [auth g]245Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2V [auth H], JA [auth h]233Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4W [auth I], KA [auth i]260Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7X [auth J], LA [auth j]247Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5Y [auth K], MA [auth k]240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1Z [auth L], NA [auth l]268Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3AA [auth M], OA [auth m]254Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth N], PA [auth n]238Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7CA [auth O], QA [auth o]276Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3DA [auth P], RA [auth p]204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2EA [auth Q], SA [auth q]201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5FA [auth R], TA [auth r]262Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1GA [auth S], UA [auth s]240Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4HA [auth T], VA [auth t]263Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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CB [auth D], EB [auth E], XA [auth A], ZA [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BB [auth C], GB [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
WA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth B], DB [auth D], FB [auth E], HB [auth F], YA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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: 2018-12-05 
  • 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  (Full details and data files)

  • Version 1.0: 2018-12-05
    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, Other