9D4C | pdb_00009d4c

Proteasome core particle assembly intermediate Blm10:alpha-ring purified from Saccharomyces cerevisiae.

• PDB DOI: https://doi.org/10.2210/pdb9D4C/pdb
• EM Map EMD-46559: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2024-08-12 Released: 2025-08-20 
• Deposition Author(s): Chen, X., Kaur, M., Roelofs, J., Walters, K.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

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 

• DOI: https://doi.org/10.1038/s41467-026-77943-w

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A1B1C1D1E1F1G1H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A8B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, gel filtration, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 472.89 kDa 
• Atom Count: 29,580 
• Modeled Residue Count: 3,731 
• Deposited Residue Count: 4,200 
• Unique protein chains: 9

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	A	252	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SCL1, PRC2, PRS2, YGL011C
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243  Go to UniProtKB:  P21243

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	B	250	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE8, PRS4, YML092C
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639  Go to UniProtKB:  P23639

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	C	258	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE9, PRS5, YGR135W
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638  Go to UniProtKB:  P23638

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	D	254	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE6, YOL038W
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303  Go to UniProtKB:  P40303

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	E	260	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PUP2, DOA5, YGR253C, G9155
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379  Go to UniProtKB:  P32379

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	F	234	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE5, YMR314W, YM9924.06
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302  Go to UniProtKB:  P40302

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	G	288	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242  Go to UniProtKB:  P21242

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	H [auth I]	261	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PUP1, YOR157C EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043  Go to UniProtKB:  P25043

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome activator BLM10	I [auth O]	2,143	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: BLM10, BLM3, YFL007W, YFL006W
UniProt
Find proteins for P43583 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43583  Go to UniProtKB:  P43583

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Chen, X., Kaur, M., Roelofs, J., Walters, K.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1 ZIA BC011490
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM149314

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Data collection, Database references
• Version 1.2: 2026-10-07
  Changes: Data collection, Database references