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 9D0T | pdb_00009d0t

Proteasome core particle assembly intermediate Blm10:13S 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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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history. 

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.

(2026) Nat Commun 

Macromolecule Content 

  • Total Structure Weight: 540.82 kDa 
  • Atom Count: 34,073 
  • Modeled Residue Count: 4,296 
  • Deposited Residue Count: 4,803 
  • Unique protein chains: 12

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1252Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP21243
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2250Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP23639
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3258Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP23638
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4254Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE6, YOL038W
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40303
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5260Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32379
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6234Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40302
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7288Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP21242
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2H [auth I]261Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP1, YOR157C
EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I [auth J]205Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP3, YER094C
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4J [auth K]198Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRE1, YER012W
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome activator BLM10K [auth O]2,143Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BLM10, BLM3, YFL007W, YFL006W
UniProt
Find proteins for P43583 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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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: UMP1, YBR173C, YBR1234, MYLK2
EC: 2.7.11.18
UniProt
Find proteins for A4IFM7 (Bos taurus)
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Find proteins for P38293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupsA4IFM7P38293
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Reference Sequence

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

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
  • Version 2.0: 2025-08-20
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Data processing, Database references, Derived calculations, Experimental preparation, Refinement description, Structure summary
  • Version 2.1: 2026-03-04
    Changes: Data collection
  • Version 2.2: 2026-10-07
    Changes: Data collection, Database references