9D4U | pdb_00009d4u

Core particle assembly intermediate Capless 13S purified from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb9D4U/pdb
• EM Map EMD-46570: EMDB EMDataResource

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


• Deposited: 2024-08-13 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: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of Blm10:13S proteasome assembly 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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A1B1C1D1E1F1G1H1I1J1K1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A10B1 

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: 294.54 kDa 
• Atom Count: 17,620 
• Modeled Residue Count: 2,273 
• Deposited Residue Count: 2,660 
• Unique protein chains: 11

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 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

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome maturation factor UMP1	K [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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.1

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