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



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:  
    5VFU, 5VFP, 5VFO, 5VFR, 5VFQ, 5VFT, 5VFS

  • 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 ...

    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 1U911Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3V480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11X380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6Y378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7Z286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 7
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26S proteasome non-ATPase regulatory subunit 13a373Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4b191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14c287Homo 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 8d257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
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Sem1e70Homo sapiensMutation(s): 0 
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Entity ID: 12
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26S protease regulatory subunit 7A361Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 13
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26S protease regulatory subunit 4B348Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 14
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26S protease regulatory subunit 8C384Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 15
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26S protease regulatory subunit 6BD380Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 16
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26S protease regulatory subunit 10BE353Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 17
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26S protease regulatory subunit 6AF377Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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Entity ID: 18
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Proteasome subunit alpha type-6Gg240Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 19
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Proteasome subunit alpha type-2Hh232Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 20
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Proteasome subunit alpha type-4Ii250Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 21
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Proteasome subunit alpha type-7Jj243Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 22
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Proteasome subunit alpha type-5Kk234Homo 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-1Ll238Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 24
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Proteasome subunit alpha type-3Mm245Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 25
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Proteasome subunit beta type-6Nn191Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 26
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Proteasome subunit beta type-7Oo220Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 27
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Proteasome subunit beta type-3Pp204Homo 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-2Qq199Homo 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-5Rr201Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 30
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Proteasome subunit beta type-1Ss213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 31
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Proteasome subunit beta type-4Tt215Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 32
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26S proteasome non-ATPase regulatory subunit 2f908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
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 

  • Version 1.0: 2018-07-18
    Type: Initial release