5VFU

Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.

Zhu, Y., Wang, W.L., Yu, D., Ouyang, Q., Lu, Y., Mao, Y.

(2018) Nat Commun 9: 1360-1360

  • DOI: 10.1038/s41467-018-03785-w
  • Primary Citation of Related Structures:  
    5VFO, 5VFP, 5VFQ, 5VFR, 5VFS, 5VFT, 5VFU

  • PubMed Abstract: 

    • The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate-translocation channel leading to the proteolytic chamber of the core particle (CP) ...

    The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate-translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme.

    Organizational Affiliation: 

    Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. youdong_mao@dfci.harvard.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth U]911Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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GTEx:  ENSG00000173692
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Entity ID: 2
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26S proteasome non-ATPase regulatory subunit 3B [auth V]480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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GTEx:  ENSG00000108344
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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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GTEx:  ENSG00000197170
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Entity ID: 4
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26S proteasome non-ATPase regulatory subunit 11D [auth X]380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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GTEx:  ENSG00000108671
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Entity ID: 5
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26S proteasome non-ATPase regulatory subunit 6E [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
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Entity ID: 6
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26S proteasome non-ATPase regulatory subunit 7F [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
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26S proteasome non-ATPase regulatory subunit 13G [auth a]373Homo 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]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14I [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
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Entity ID: 10
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26S proteasome non-ATPase regulatory subunit 8J [auth d]257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Sem1K [auth e]70Homo sapiensMutation(s): 0 
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26S protease regulatory subunit 7L [auth A]361Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
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26S protease regulatory subunit 4M [auth B]348Homo sapiensMutation(s): 0 
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26S protease regulatory subunit 8N [auth C]384Homo sapiensMutation(s): 0 
Gene Names: PSMC5, SUG1
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26S protease regulatory subunit 6BO [auth D]380Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
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26S protease regulatory subunit 10BP [auth E]353Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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26S protease regulatory subunit 6AQ [auth F]377Homo sapiensMutation(s): 0 
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Entity ID: 18
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Proteasome subunit alpha type-6R [auth G], FA [auth g]240Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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Entity ID: 19
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Proteasome subunit alpha type-2S [auth H], GA [auth h]232Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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Proteasome subunit alpha type-4T [auth I], HA [auth i]250Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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Entity ID: 21
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Proteasome subunit alpha type-7U [auth J], IA [auth j]243Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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Entity ID: 22
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Proteasome subunit alpha type-5V [auth K], JA [auth k]234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 23
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Proteasome subunit alpha type-1W [auth L], KA [auth l]238Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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Entity ID: 24
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Proteasome subunit alpha type-3X [auth M], LA [auth m]245Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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Entity ID: 25
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Proteasome subunit beta type-6Y [auth N], MA [auth n]191Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
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Entity ID: 26
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Proteasome subunit beta type-7Z [auth O], NA [auth o]220Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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Entity ID: 27
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Proteasome subunit beta type-3AA [auth P], OA [auth p]204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 28
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Proteasome subunit beta type-2BA [auth Q], PA [auth q]199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 29
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Proteasome subunit beta type-5CA [auth R], QA [auth r]201Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
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Entity ID: 30
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Proteasome subunit beta type-1DA [auth S], RA [auth s]213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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Entity ID: 31
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Proteasome subunit beta type-4EA [auth T], SA [auth t]215Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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Entity ID: 32
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26S proteasome non-ATPase regulatory subunit 2TA [auth f]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
UA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Source and taxonomy