9CMR | pdb_00009cmr

Saccharomyces cerevisiae Tom1 HECT domain

PDB DOI: https://doi.org/10.2210/pdb9CMR/pdb

Classification: LIGASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-15 Released: 2025-05-28
Deposition Author(s): Schubert, H.L., Hill, C.P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.258 (Depositor), 0.257 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CMR

This is version 1.2 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: 47.91 kDa
Atom Count: 3,346
Modeled Residue Count: 407
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TOM1	A	412	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.258 (Depositor), 0.257 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 298.998	α = 90
b = 298.998	β = 90
c = 298.998	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release
Version 1.1: 2025-12-10
Changes: Database references
Version 1.2: 2026-04-22
Changes: Database references

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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.