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.M., 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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9MHP

This is version 1.1 of the entry. See complete history.

Literature

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

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

(2024) Elife

DOI: https://doi.org/10.7554/elife.101393.1

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03280
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release
Version 1.1: 2026-04-22
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.