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- PDB-9eld: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase T... -

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Basic information

Entry
Database: PDB / ID: 9eld
TitleFull-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p in an open-conformation
ComponentsE3 ubiquitin-protein ligase TOM1
KeywordsTRANSFERASE / cell cycle / stress response / solenoid / E3 ubiquitin ligase / RNA / GENE REGULATION
Function / homology
Function and homology information


endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / HECT-type E3 ubiquitin transferase / nucleocytoplasmic transport / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleus organization / regulation of cell size / Antigen processing: Ubiquitination & Proteasome degradation / mRNA transport / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / HECT-type E3 ubiquitin transferase / nucleocytoplasmic transport / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleus organization / regulation of cell size / Antigen processing: Ubiquitination & Proteasome degradation / mRNA transport / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Neutrophil degranulation / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleolus / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) ...E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TOM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsMadrigal, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM064649 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170856 United States
CitationJournal: Elife / Year: 2024
Title: Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters
Authors: Madrigal, J. / Schubert, H.L. / Sdano, M.A. / McCullough, L. / Connell, Z. / Formosa, T. / Hill, C.P.
History
DepositionDec 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TOM1


Theoretical massNumber of molelcules
Total (without water)376,9601
Polymers376,9601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein E3 ubiquitin-protein ligase TOM1 / HECT-type E3 ubiquitin transferase TOM1 / Suppressor of snRNA protein 2 / Temperature-dependent ...HECT-type E3 ubiquitin transferase TOM1 / Suppressor of snRNA protein 2 / Temperature-dependent organization in mitotic nucleus protein 1


Mass: 376959.844 Da / Num. of mol.: 1 / Mutation: Internal tag insertion between 1074-1075
Source method: isolated from a genetically manipulated source
Details: Internal tag insertion between 1074-1075 of the native sequence: SGGGGGGSRHHHHHHHHHHHH
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: 10293-12XHIS / Gene: TOM1, SSR2, YDR457W, D8035.1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): 10293-12XHIS
References: UniProt: Q03280, HECT-type E3 ubiquitin transferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.377 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 10293-12XHIS
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 10293-12XHIS
Buffer solutionpH: 7.5
Details: 5% glycerol, 50 mM TrisCl pH 7.5, 150 mM NaCl, 2 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. 2.5 uL of sample was applied to grids and blotted for 2.5 seconds before vitrification by ...Details: Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. 2.5 uL of sample was applied to grids and blotted for 2.5 seconds before vitrification by plunging into liquid ethane.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2000 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16098 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 7.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421924
ELECTRON MICROSCOPYf_angle_d0.71829673
ELECTRON MICROSCOPYf_dihedral_angle_d6.6972892
ELECTRON MICROSCOPYf_chiral_restr0.0693438
ELECTRON MICROSCOPYf_plane_restr0.0063752

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