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



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
Find proteins for Q99460 (Homo sapiens)
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GTEx  ENSG00000173692
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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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PHAROS  O43242
GTEx  ENSG00000108344
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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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PHAROS  O00232
GTEx  ENSG00000197170
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11X380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
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GTEx  ENSG00000108671
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6Y378Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
Find proteins for Q15008 (Homo sapiens)
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GTEx  ENSG00000163636
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7Z286Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
Find proteins for P51665 (Homo sapiens)
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GTEx  ENSG00000103035
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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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GTEx  ENSG00000185627
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4b191Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens)
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GTEx  ENSG00000159352
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Entity ID: 9
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26S proteasome non-ATPase regulatory subunit 14c287Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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GTEx  ENSG00000115233
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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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GTEx  ENSG00000099341
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Entity ID: 11
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Sem1e70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
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GTEx  ENSG00000127922
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Entity ID: 12
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Proteasome subunit alpha type-6G, g240Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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GTEx  ENSG00000100902
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Entity ID: 13
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Proteasome subunit alpha type-2H, h232Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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GTEx  ENSG00000106588
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Entity ID: 14
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Proteasome subunit alpha type-4I, i250Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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GTEx  ENSG00000041357
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Entity ID: 15
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Proteasome subunit alpha type-7J, j243Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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GTEx  ENSG00000101182
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Entity ID: 16
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Proteasome subunit alpha type-5K, k234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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GTEx  ENSG00000143106
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Entity ID: 17
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Proteasome subunit alpha type-1L, l238Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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GTEx  ENSG00000129084
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Entity ID: 18
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Proteasome subunit alpha type-3M, m245Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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GTEx  ENSG00000100567
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Entity ID: 19
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Proteasome subunit beta type-6N, n191Homo 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-7O, o220Homo 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-3P, p204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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GTEx  ENSG00000277791
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Entity ID: 22
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Proteasome subunit beta type-2Q, q199Homo 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-5R, r201Homo 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
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1S, s213Homo 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
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Proteasome subunit beta type-4T, t215Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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GTEx  ENSG00000159377
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7A399Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
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GTEx  ENSG00000161057
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Entity ID: 27
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26S proteasome regulatory subunit 4B389Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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GTEx  ENSG00000100764
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Entity ID: 28
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26S proteasome regulatory subunit 8C392Homo sapiensMutation(s): 0 
Gene Names: PSMC5, SUG1
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GTEx  ENSG00000087191
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Entity ID: 29
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26S proteasome regulatory subunit 6BD380Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
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GTEx  ENSG00000013275
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Entity ID: 30
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26S proteasome regulatory subunit 10BE375Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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Entity ID: 31
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26S proteasome regulatory subunit 6AF396Homo sapiensMutation(s): 0 
Gene Names: PSMC3, TBP1
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GTEx  ENSG00000165916
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Entity ID: 32
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26S proteasome non-ATPase regulatory subunit 2f908Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
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GTEx  ENSG00000175166
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
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A, B, D, F
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
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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 

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