5VFP

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
Proteasome subunit alpha type-6A [auth G], Y [auth g]240Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B [auth H], Z [auth h]232Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C [auth I], AA [auth i]250Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D [auth J], BA [auth j]243Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E [auth K], CA [auth k]234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F [auth L], DA [auth l]238Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G [auth M], EA [auth m]245Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6H [auth N], FA [auth n]191Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I [auth O], GA [auth o]220Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 10
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Proteasome subunit beta type-3J [auth P], HA [auth p]204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 11
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Proteasome subunit beta type-2K [auth Q], IA [auth q]199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L [auth R], JA [auth r]201Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1M [auth S], KA [auth s]213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4N [auth T], LA [auth t]215Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 15
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26S proteasome non-ATPase regulatory subunit 1O [auth U]911Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Entity ID: 16
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26S proteasome non-ATPase regulatory subunit 3P [auth V]480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Entity ID: 17
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26S proteasome non-ATPase regulatory subunit 12Q [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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Entity ID: 18
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26S proteasome non-ATPase regulatory subunit 6R [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 19
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26S proteasome non-ATPase regulatory subunit 7S [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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Entity ID: 20
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26S proteasome non-ATPase regulatory subunit 13T [auth a]373Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 21
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26S proteasome non-ATPase regulatory subunit 4U [auth b]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 22
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26S proteasome non-ATPase regulatory subunit 14V [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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Entity ID: 23
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26S proteasome non-ATPase regulatory subunit 8W [auth d]257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 24
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sem1X [auth e]70Homo sapiensMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11MA [auth X]380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 26
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26S proteasome regulatory subunit 7NA [auth A]399Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4OA [auth B]389Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Entity ID: 28
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26S proteasome regulatory subunit 8PA [auth C]392Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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Entity ID: 29
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26S proteasome regulatory subunit 6BQA [auth D]380Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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Entity ID: 30
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26S proteasome regulatory subunit 10BRA [auth E]375Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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Entity ID: 31
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26S proteasome regulatory subunit 6ASA [auth F]396Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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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: PSMD2TRAP2
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
VA [auth A], WA [auth D], XA [auth E], YA [auth F]PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
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: 4.20 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