5VFR

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 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
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
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth V]480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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Find proteins for O43242 (Homo sapiens)
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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
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
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GTEx:  ENSG00000163636
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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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Entity ID: 7
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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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Entity ID: 11
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Sem1K [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
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Entity ID: 12
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Proteasome subunit alpha type-6L [auth G], Z [auth g]240Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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Entity ID: 13
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Proteasome subunit alpha type-2M [auth H], AA [auth h]232Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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Entity ID: 14
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Proteasome subunit alpha type-4N [auth I], BA [auth i]250Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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Entity ID: 15
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Proteasome subunit alpha type-7O [auth J], CA [auth j]243Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5P [auth K], DA [auth k]234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 17
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Proteasome subunit alpha type-1Q [auth L], EA [auth l]238Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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Entity ID: 18
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Proteasome subunit alpha type-3R [auth M], FA [auth m]245Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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Entity ID: 19
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Proteasome subunit beta type-6S [auth N], GA [auth n]191Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
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GTEx:  ENSG00000142507
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Entity ID: 20
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Proteasome subunit beta type-7T [auth O], HA [auth o]220Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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GTEx:  ENSG00000136930
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Entity ID: 21
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Proteasome subunit beta type-3U [auth P], IA [auth p]204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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GTEx:  ENSG00000277791
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Entity ID: 22
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Proteasome subunit beta type-2V [auth Q], JA [auth q]199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067
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Entity ID: 23
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Proteasome subunit beta type-5W [auth R], KA [auth r]201Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
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GTEx:  ENSG00000100804
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Entity ID: 24
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Proteasome subunit beta type-1X [auth S], LA [auth s]213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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GTEx:  ENSG00000008018
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4Y [auth T], MA [auth t]215Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7NA [auth A]399Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
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Entity ID: 27
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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: PSMC5, SUG1
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Entity ID: 29
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26S proteasome regulatory subunit 6BQA [auth D]380Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
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Entity ID: 30
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26S proteasome regulatory subunit 10BRA [auth E]375Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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Entity ID: 31
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26S proteasome regulatory subunit 6ASA [auth F]396Homo sapiensMutation(s): 0 
Gene Names: PSMC3, TBP1
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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 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 B], XA [auth D], 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: 4.90 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