9MHP | pdb_00009mhp

cryo-EM structure of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture

• PDB DOI: https://doi.org/10.2210/pdb9MHP/pdb
• EM Map EMD-48280: EMDB EMDataResource

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


• Deposited: 2024-12-12 Released: 2025-10-01 
• Deposition Author(s): Madrigal, J.A., Schubert, H.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters

Madrigal, J.A., Schubert, H.L., Sdano, M.A., McCullough, L., Connell, Z., Formosa, T.G., Hill, C.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 376.74 kDa 
• Atom Count: 21,652 
• Modeled Residue Count: 2,703 
• Deposited Residue Count: 3,287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TOM1	A	3,287	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TOM1, SSR2, YDR457W, D8035.1 EC: 2.3.2.26
UniProt
Find proteins for Q03280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03280  Go to UniProtKB:  Q03280

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Madrigal, J.A., Schubert, H.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170856
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM064649

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release