6XMJ

Human 20S proteasome bound to an engineered 11S (PA26) activator

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

The Y Phi motif defines the structure-activity relationships of human 20S proteasome activators.

Opoku-Nsiah, K.A., de la Pena, A.H., Williams, S.K., Chopra, N., Sali, A., Lander, G.C., Gestwicki, J.E.

(2022) Nat Commun 13: 1226-1226

  • DOI: 10.1038/s41467-022-28864-x
  • Primary Citation of Related Structures:  
    6XMJ

  • PubMed Abstract: 

    • The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S) ...

    The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S). Here, we synthesize and screen ~120 HbYX-like peptides, revealing unexpected differences from the archaeal system and defining the h20S recognition sequence as the Y-F/Y (YФ) motif. To gain further insight, we create a functional chimera of the optimized sequence, NLSYYT, fused to the model activator, PA26 E102A . A cryo-EM structure of PA26 E102A -h20S is used to identify key interactions, including non-canonical contacts and gate-opening mechanisms. Finally, we demonstrate that the YФ sequence preferences are tuned by valency, allowing multivalent PAs to sample greater sequence space. These results expand the model for termini-mediated gating and provide a template for the design of h20S activators.

    Organizational Affiliation: 

    Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, USA. jason.gestwicki@ucsf.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6A244Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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PHAROS:  P60900
GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B233Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C250Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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UniProt GroupP25789
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D243Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F238Homo 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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G245Homo 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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6H202Homo 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: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I220Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L201Homo 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: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1M213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4N217Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome activator protein PA26
O, P, Q, R, S, T, U
O, P, Q, R, S, T, U
228Trypanosoma bruceiMutation(s): 3 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2-EB020402
American Cancer SocietyUnited States132279-PF-18-189-01- DMC

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references