9D0T | pdb_00009d0t

Core particle assembly intermediate 1 purified from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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Literature

Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle.

Kaur, M.Chen, X.Lee, S.Y.Weaver, T.M.Freudenthal, B.D.Walters, K.J.Roelofs, J.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.11.04.621988
  • Primary Citation of Related Structures:  
    9D0T

  • PubMed Abstract: 

    Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be replaced by Blm10 to form Blm10:CP, which promotes ATP-independent degradation of disordered proteins. Here, we present evidence of distinct parallel assembly pathways for CP by solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model of Blm10 and Pba1/Pba2 sequential activity in a single assembly pathway, as we find their CP binding is mutually exclusive and both are present on early and late assembly intermediates. CP affinity for Pba1/Pba2 is reduced during maturation, promoting Pba1/Pba2 release. We find Blm10 undergoes no such affinity switch, suggesting this pathway predominantly yields mature Blm10-bound CP. Altogether, our findings conflict with the current paradigm of sequential CP binding to instead indicate parallel assembly pathways by Pba1/Pba2 and Blm10.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., HLSIC 1077, Kansas, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1252Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
UniProt
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UniProt GroupP21243
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2250Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE8PRS4YML092C
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3258Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
UniProt
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UniProt GroupP23638
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4254Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE6YOL038W
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40303
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5260Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
UniProt
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UniProt GroupP32379
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6234Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7288Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
UniProt
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UniProt GroupP21242
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2H [auth I]261Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I [auth J]205Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP3YER094C
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4J [auth K]198Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE1YER012W
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator BLM10K [auth O]2,143Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BLM10BLM3YFL007WYFL006W
UniProt
Find proteins for P43583 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome maturation factor UMP1,Myosin light chain kinase 2, skeletal/cardiac muscleL [auth P]200Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UMP1YBR173CYBR1234MYLK2
EC: 2.7.11.18
UniProt
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Find proteins for P38293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupsP38293A4IFM7
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1 ZIA BC011490
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM149314

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release