9D3I | pdb_00009d3i

Proteasome core particle assembly intermediate 5-alpha/4-beta/Ump1 purified from Saccharomyces cerevisiae.

• PDB DOI: https://doi.org/10.2210/pdb9D3I/pdb
• EM Map EMD-46535: EMDB EMDataResource

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


• Deposited: 2024-08-10 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: 3.11 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 10-mer - A1B1C1D1E1F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A9B1 

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: 263.83 kDa 
• Atom Count: 15,673 
• Modeled Residue Count: 2,004 
• Deposited Residue Count: 2,381 
• Unique protein chains: 10

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
Probable proteasome subunit alpha type-7	E [auth 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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome maturation factor UMP1	F [auth P]	200	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UMP1, YBR173C, YBR1234
UniProt
Find proteins for P38293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38293  Go to UniProtKB:  P38293

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	G [auth H]	215	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE3, YJL001W, J1407 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624  Go to UniProtKB:  P38624

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 subunit beta type-3	I [auth J]	205	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PUP3, YER094C
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451  Go to UniProtKB:  P25451

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	J [auth K]	198	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRE1, YER012W
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141  Go to UniProtKB:  P22141

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

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