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- EMDB-48145: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase T... -

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Basic information

Entry
Database: EMDB / ID: EMD-48145
TitleFull-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p in an open-conformation
Map datacryo-EM unsharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an open-conformation state.
Sample
  • Complex: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
    • Protein or peptide: E3 ubiquitin-protein ligase TOM1
Keywordscell cycle / stress response / solenoid / E3 ubiquitin ligase / RNA / GENE REGULATION / TRANSFERASE
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) / regulation of cell size / nucleus organization / 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) / regulation of cell size / nucleus organization / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsMadrigal JM
Funding support United States, 2 items
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 HL / Sdano MA / McCullough L / Connell Z / Formosa T / Hill CP
History
DepositionDec 4, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48145.png

Downloads & links

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Map

FileDownload / File: emd_48145.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM unsharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an open-conformation state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 256 pix.
= 387.2 Å		1.51 Å/pix.
x 256 pix.
= 387.2 Å		1.51 Å/pix.
x 256 pix.
= 387.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.1663175 - 0.6558617
Average (Standard dev.)0.00095646107 (±0.02549675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 387.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48145_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half-map A of full-length and internally HIS-tagged...

Fileemd_48145_half_map_1.map
Annotationcryo-EM half-map A of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an open-conformation state.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half-map B of full-length and internally HIS-tagged...

Fileemd_48145_half_map_2.map
Annotationcryo-EM half-map B of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an open-conformation state.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p

EntireName: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
Components
  • Complex: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
    • Protein or peptide: E3 ubiquitin-protein ligase TOM1

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Supramolecule #1: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p

SupramoleculeName: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 10293-12XHIS
Molecular weightTheoretical: 377 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase TOM1

MacromoleculeName: E3 ubiquitin-protein ligase TOM1 / type: protein_or_peptide / ID: 1
Details: Internal tag insertion between 1074-1075 of the native sequence: SGGGGGGSRHHHHHHHHHHHH
Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 10293-12XHIS
Molecular weightTheoretical: 376.959844 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR MDGLLLKVAE KYKYKQDPKK ECEVKLVEM EAHDVDYCLK MLKFTRRLLL NTENRFVYSS GDVLMYLLNC PNFTIKLAVM RILAILGERF VIAREKIVAH N IFGDHNLR ...String:
MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR MDGLLLKVAE KYKYKQDPKK ECEVKLVEM EAHDVDYCLK MLKFTRRLLL NTENRFVYSS GDVLMYLLNC PNFTIKLAVM RILAILGERF VIAREKIVAH N IFGDHNLR KKTLKLALSL SSSVMDEDGE HFSLVDLYFD KKKVPQKWRK LRFTHYTSND FKKSSQQKNN INETQTSIKK VT MTTQELC EHSLQQIFDK GMALLPAESW FDFSIKASVA KAFSDDSGEN IDLRNIIIET KLNAIAFVNT IFSPPQVSSK LFE LDPYAF NSLTDLISLS ETKIPKELRT DALFTLECIS LKHVWCSDII RNLGGNISHG LLFQILRYIA KTLREATDEI DEEY NVRFF YLISNLADVK PLHESLFAAG LIPTLLEIVS IRNCPYKRTL ASATHLLETF IDNSETTTEF IENDGFTMLI TSVAN EIDF TLAHPETWQP PKYSVVYYSI SFRELAYIRS LLKLVLKLLS TDSGDRIRNL IDSPILVSLK KILENKLVFG LTLITY TLD VVQKVINSEP TIYPVLVEAG LIPYVIDNFP KLIGPSAELL SLLPDVVSAI CLNPEGLKQV KEKGLINNLF DFLLDAD HA RILTGGDRST EYGTDIDELA RHYPDLKANI VEALCNVIRK MPSTFRNERE FLFTSPKDQK YFFHRKNEEI LTDKEEHE P AYWELLDKGT MLDTFTSVLF GMSLGNGSFS QVPQHLEARD FLAIIFMENP PYEYFTSVAI SNVTEVLQYL DEKYEDYAF MDVMKVLNDQ LENLNDFLNS PNDRSFFLER DGENSVRSCH SKLCRLAAIL NIVTNVYIDL TTLSCKRIMQ IYSYFDKRGF SLIKNLKLL FQKCALEEMY IRQHMPDSVI TETMPLPIVD VSGDGPPLQI YIDDPKKGDQ KGKITSVKTR NTLQMRTILY T LQSNTAIL FRCFLRLSHS RNMDLEHKDL TTEVHIFENV VENVIEMLKA TELEGHLPYI LVLLNFNTFV FTIPKASPNS TE ILQTIPA YIFYQKGGYL LYLHIIRDLF TRMTKIKSGG GGGGSRHHHH HHHHHHHHDL SSLDNINYID ESNGILTLSC LIN ALTFYN KSMQTETMEN VQSIGKYYVS IDDDYNIMKA LTVPIKVMAL AMILDLDKSD SLFKTQSRNV PYSVFKQLLS MLKN IFTNV NIYTKELYEL HWDLIFPPIK KISLFEQVGI PGDVAANYLT DTGDDLPADN SIGLFSPEQW EKYKKLIGED KSIYY PQPM QAQYYKGCSS KELDELRDTF FNDGLPSRIF TVLPFYPKLV NAFAKTLLQI FTKYDEPTEV FAGRILDRIL ETDLDD PAT LSSLIHLFGI FLNEKYIYQK ASHLMQRFIE YLEKSLKPEH VNTPWFSKAL YVYEIILAKS ELPHLEELSK DVLLRYP LL SMAKVFRIPD PMKQKLFDIL IRVSDISNFY SALATSRILI FYSRDELYAN NIARSGILSR LLKVIGSFQK LDKINFLE S SFLLLTRRCF ETTENVDALI RAEINRSFTA RPLGGGDDAV RELTTILEEK AHVVMRSPSQ FIDVLCETAR FHEFDDQGA LVDYSLKRFL GEKDKNTQAS STEKSDIYER TGIMHLLLSQ LMAASEKDWL SEPANSSDLP ENKKAQLDPS RNPVCAYMIF LLKLLVELV SSYNQCKFEF LTFSRRNTYA ERPRPRTTAI NFFLYRLLDK PVGTDHDKHE AKRREVIGML ARSVIIGFLA T VQDDRTTK TDVKLADPHM NFIRKFAIEA IIKAIRNATS SSKLLESNHL KLDMWFRIIT SMVYVQAPYL RQLLDSNKVE AD QYQLCKL VIDLGLPSVI TEAMASIDLN YPFSKKIFNV AVEALNTISS TRNNFSEHFK IEDHDEVEDE VDESDKEEIP DMF KNSALG MYDVEDIEED DDDDTSLIGD DDAMAFVDSD NGFEVVFSDE DDDMGEEDAD DARSDSEENE LSSEMQSSTA DGTD VDYEV DDADGLIINI DQPSGDDEEM ADYDANISHS SHSENEDDAS MDVIEVYDDE LSSGYDVDLS DYDVDESDWD SGLSS LSIS DEDSESSEDE PINSTRMGDS RRRWLIAEGV ELTDDSQGES EEDDRGVFRG IEHIFSNENE PLFRVHDEMR HRNHHR SIN RTHFHSAMSA PSLSLLNRGR RNQSNLINPL GPTGLEQVEN DISDQVTVAG SGSRPRSHHL HFSEVLVSGS FFDEPVL DG IILKSTVSRW KDIFDMFYDS KTYANCIIPT VINRLYKVSL ALQKDLENKR EQEKLKNKNL LFNEAKVESH NSSDAISV E QDDIQESNVT HDDHEPVYVT IQGSEVDIGG TDIDPEFMNA LPDDIRADVF AQHVRERRAE ARLNSDHNVH SREIDSDFL EAIPEDIREG ILDTEAEEQR MFGRIGSSAD VIRADDDVSN NDEEVENGLD HGNSNDRNNA DPEKKKPARI YFAPLIDRAG IASLMKSVF ISKPYIQREI YHELFYRLCS SKQNRNDLMN TFLFILSEGI IDQHSLEKVY NIISSRAMGH AKTTTVRQLP S DCTPLTVA NQTIEILQSL IDADSRLKYF LIAEHDNLIV NKANNKSRKE ALPDKKLRWP LWHLFSLLDR KLITDESVLM DL LTRILQV CTKTLAVLST SSNGKENLSK KFHLPSFDED DLMKILSIIM LDSCTTRVFQ QTLNIIYNLS KLQGCMSIFT KHL VSLAIS IMSKLKSALD GLSREVGTIT TGMEINSELL QKFTLPSSDQ AKLLKILTTV DFLYTHKRKE EERNVKDLQS LYDK MNGGP VWSSLSECLS QFEKSQAINT SATILLPLIE SLMVVCRRSD LSQNRNTAVK YEDAKLLDFS KTRVENLFFP FTDAH KKLL NQMIRSNPKL MSGPFALLVK NPKVLDFDNK RYFFNAKLKS DNQERPKLPI TVRREQVFLD SYRALFFKTN DEIKNS KLE ITFKGESGVD AGGVTREWYQ VLSRQMFNPD YALFLPVPSD KTTFHPNRTS GINPEHLSFF KFIGMIIGKA IRDQCFL DC HFSREVYKNI LGRPVSLKDM ESLDPDYYKS LVWILENDIT DIIEETFSVE TDDYGEHKVI NLIEGGKDII VTEANKQD Y VKKVVEYKLQ TSVKEQMDNF LVGFYALISK DLITIFDEQE LELLISGLPD IDVDDWKNNT TYVNYTATCK EVSYFWRAV RSFDAEERAK LLQFVTGTSK VPLNGFKELS GVNGVCKFSI HRDFGSSERL PSSHTCFNQL NLPPYESYET LRGSLLLAIN EGHEGFGLA

UniProtKB: E3 ubiquitin-protein ligase TOM1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 5% glycerol, 50 mM TrisCl pH 7.5, 150 mM NaCl, 2 mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
DetailsSpecimens 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16098
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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