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- EMDB-48280: cryo-EM structure of full-length and internally HIS-tagged yeast ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48280
Titlecryo-EM structure of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture
Map datacryo-EM sharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture.
Sample
  • Complex: yeast E3 ubiquitin ligase Tom1p
    • Protein or peptide: E3 ubiquitin-protein ligase TOM1
Keywordscell 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) / 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: 3.97 Å
AuthorsMadrigal JA / Schubert HL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170856 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM064649 United States
CitationJournal: To Be Published
Title: Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters
Authors: Madrigal JA / Schubert HL / Sdano MA / McCullough L / Connell Z / Formosa TG / Hill CP
History
DepositionDec 12, 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_48280.png

Downloads & links

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Map

FileDownload / File: emd_48280.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM sharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture.
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: 0.3
Minimum - Maximum-1.3385649 - 2.0940485
Average (Standard dev.)0.00067460607 (±0.047058415)
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_48280_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM unsharpened map of full-length and internally HIS-tagged...

Fileemd_48280_additional_1.map
Annotationcryo-EM unsharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture.
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_48280_half_map_1.map
Annotationcryo-EM half-map A of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture.
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_48280_half_map_2.map
Annotationcryo-EM half-map B of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast E3 ubiquitin ligase Tom1p

EntireName: yeast E3 ubiquitin ligase Tom1p
Components
  • Complex: yeast E3 ubiquitin ligase Tom1p
    • Protein or peptide: E3 ubiquitin-protein ligase TOM1

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Supramolecule #1: yeast E3 ubiquitin ligase Tom1p

SupramoleculeName: yeast E3 ubiquitin ligase Tom1p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p
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: 376.741594 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: VLFTRCEKAR KEKLAAGYKP LVDYLIDCDT PTFLERIEAI QEWDRSRDDL YVWIPILDRM DGLLLKVAEK YKYKQDPKKE CEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN I FGDHNLRK ...String:
VLFTRCEKAR KEKLAAGYKP LVDYLIDCDT PTFLERIEAI QEWDRSRDDL YVWIPILDRM DGLLLKVAEK YKYKQDPKKE CEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN I FGDHNLRK KTLKLALSLS SSVMDEDGEH FSLVDLYFDK KKVPQKWRKL RFTHYTSNDF KKSSQQKNNI NETQTSIKKV TM TTQELCE HSLQQIFDKG MALLPAESWF DFSIKASVAK AFSDDSGENI DLRNIIIETK LNAIAFVNTI FSPPQVSSKL FEL DPYAFN SLTDLISLSE TKIPKELRTD ALFTLECISL KHVWCSDIIR NLGGNISHGL LFQILRYIAK TLREATDEID EEYN VRFFY LISNLADVKP LHESLFAAGL IPTLLEIVSI RNCPYKRTLA SATHLLETFI DNSETTTEFI ENDGFTMLIT SVANE IDFT LAHPETWQPP KYSVVYYSIS FRELAYIRSL LKLVLKLLST DSGDRIRNLI DSPILVSLKK ILENKLVFGL TLITYT LDV VQKVINSEPT IYPVLVEAGL IPYVIDNFPK LIGPSAELLS LLPDVVSAIC LNPEGLKQVK EKGLINNLFD FLLDADH AR ILTGGDRSTE YGTDIDELAR HYPDLKANIV EALCNVIRKM PSTFRNEREF LFTSPKDQKY FFHRKNEEIL TDKEEHEP A YWELLDKGTM LDTFTSVLFG MSLGNGSFSQ VPQHLEARDF LAIIFMENPP YEYFTSVAIS NVTEVLQYLD EKYEDYAFM DVMKVLNDQL ENLNDFLNSP NDRSFFLERD GENSVRSCHS KLCRLAAILN IVTNVYIDLT TLSCKRIMQI YSYFDKRGFS LIKNLKLLF QKCALEEMYI RQHMPDSVIT ETMPLPIVDV SGDGPPLQIY IDDPKKGDQK GKITSVKTRN TLQMRTILYT L QSNTAILF RCFLRLSHSR NMDLEHKDLT TEVHIFENVV ENVIEMLKAT ELEGHLPYIL VLLNFNTFVF TIPKASPNST EI LQTIPAY IFYQKGGYLL YLHIIRDLFT RMTKIKSGGG GGGSRHHHHH HHHHHHHLSS LDNINYIDES NGILTLSCLI NAL TFYNKS MQTETMENVQ SIGKYYVSID DDYNIMKALT VPIKVMALAM ILDLDKSDSL FKTQSRNVPY SVFKQLLSML KNIF TNVNI YTKELYELHW DLIFPPIKKI SLFEQVGIPG DVAANYLTDT GDDLPADNSI GLFSPEQWEK YKKLIGEDKS IYYPQ PMQA QYYKGCSSKE LDELRDTFFN DGLPSRIFTV LPFYPKLVNA FAKTLLQIFT KYDEPTEVFA GRILDRILET DLDDPA TLS SLIHLFGIFL NEKYIYQKAS HLMQRFIEYL EKSLKPEHVN TPWFSKALYV YEIILAKSEL PHLEELSKDV LLRYPLL SM AKVFRIPDPM KQKLFDILIR VSDISNFYSA LATSRILIFY SRDELYANNI ARSGILSRLL KVIGSFQKLD KINFLESS F LLLTRRCFET TENVDALIRA EINRSFTARP LGGGDDAVRE LTTILEEKAH VVMRSPSQFI DVLCETARFH EFDDQGALV DYSLKRFLGE RDKNTQASST EKSDIYERTG IMHLLLSQLM AASEKDWLSE PANSSDLPEN KKAQLDPSRN PVCAYMIFLL KLLVELVSS YNQCKFEFLT FSRRNTYAER PRPRTTAINF FLYRLLDKPV GTDHDKHEAK RREVIGMLAR SVIIGFLATV Q DDRTTKTD VKLADPHMNF IRKFAIEAII KAIRNATSSS KLLESNHLKL DMWFRIITSM VYVQAPYLRQ LLDSNKVEAD QY QLCKLVI DLGLPSVITE AMASIDLNYP FSKKIFNVAV EALNTISSTR NNFSEHFKIE DHDEVEDEVD ESDKEEIPDM FKN SALGMY DVEDIEEDDD DDTSLIGDDD AMAFVDSDNG FEVVFSDEDD DMGEEDADDA RSDSEENELS SEMQSSTADG TDVD YEVDD ADGLIINIDQ PSGDDEEMAD YDANISHSSH SENEDDASMD VIEVYDDELS SGYDVDLSDY DVDESDWDSG LSSLS ISDE DSESSEDEPI NSTRMGDSRR RWLIAEGVEL TDDSQGESEE DDRGVFRGIE HIFSNENEPL FRVHDEMRHR NHHRSI NRT HFHSAMSAPS LSLLNRGRRN QSNLINPLGP TGLEQVENDI SDQVTVAGSG SRPRSHHLHF SEVLVSGSFF DEPVLDG II LKSTVSRWKD IFDMFYDSKT YANCIIPTVI NRLYKVSLAL QKDLENKREQ EKLKNKNLLF NEAKVESHNS SDAISVEQ D DIQESNVTHD DHEPVYVTIQ GSEVDIGGTD IDPEFMNALP DDIRADVFAQ HVRERRAEAR LNSDHNVHSR EIDSDFLEA IPEDIREGIL DTEAEEQRMF GRIGSSADVI RADDDVSNND EEVENGLDHG NSNDRNNADP EKKKPARIYF APLIDRAGIA SLMKSVFIS KPYIQREIYH ELFYRLCSSK QNRNDLMNTF LFILSEGIID QHSLEKVYNI ISSRAMGHAK TTTVRQLPSD C TPLTVANQ TIEILQSLID ADSRLKYFLI AEHDNLIVNK ANNKSRKEAL PDKKLRWPLW HLFSLLDRKL ITDESVLMDL LT RILQVCT KTLAVLSTSS NGKENLSKKF HLPSFDEDDL MKILSIIMLD SCTTRVFQQT LNIIYNLSKL QGCMSIFTKH LVS LAISIM SKLKSALDGL SREVGTITTG MEINSELLQK FTLPSSDQAK LLKILTTVDF LYTHKRKEEE RNVKDLQSLY DKMN GGPVW SSLSECLSQF EKSQAINTSA TILLPLIESL MVVCRRSDLS QNRNTAVKYE DAKLLDFSKT RVENLFFPFT DAHKK LLNQ MIRSNPKLMS GPFALLVKNP KVLDFDNKRY FFNAKLKSDN QERPKLPITV RREQVFLDSY RALFFKTNDE IKNSKL EIT FKGESGVDAG GVTREWYQVL SRQMFNPDYA LFLPVPSDKT TFHPNRTSGI NPEHLSFFKF IGMIIGKAIR DQCFLDC HF SREVYKNILG RPVSLKDMES LDPDYYKSLV WILENDITDI IEETFSVETD DYGEHKVINL IEGGKDIIVT EANKQDYV K KVVEYKLQTS VKEQMDNFLV GFYALISKDL ITIFDEQELE LLISGLPDID VDDWKNNTTY VNYTATCKEV SYFWRAVRS FDAEERAKLL QFVTGTSKVP LNGFKELSGV NGVCKFSIHR DFGSSERLPS SHTCFNQLNL PPYESYETLR GSLLLAINEG HEGFGLA

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

Concentration0.5 mg/mL
BufferpH: 7.5
Details: 5 percent glycerol, 50 mM TrisCl pH 7.5, 150 mM NaCl, 2 mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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

Particle selectionDetails: 3,522 of 3,630 micrographs were selected for particle picking from grids containing Tom1pHis. Initial blob picks were curated via 2D-classification and 3D ab initio jobs to create 60 2D ...Details: 3,522 of 3,630 micrographs were selected for particle picking from grids containing Tom1pHis. Initial blob picks were curated via 2D-classification and 3D ab initio jobs to create 60 2D templates for template-picking. 1,434,189 template-picked particles (lowpass filter 15 A) were narrowed through 6 rounds of 2D classification to give 201,930 particles, which were input to ab initio volume creation with 4 classes. 41,253 particles from one of these classes were used to refine the open/intermediate conformations and 160,667 total particles from the remaining 3 classes were combined for further refinement of the closed conformation map.
CTF correctionDetails: Movies were motion-corrected for all 3 datasets using CryoSPARC Patch Motion Correction. CTF estimation was performed on motion-corrected micrographs using CryoSPARC Patch CTF with default parameters applied.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial blob picks were curated via 2D-classification and 3D ab initio jobs to create 60 2D templates for template-picking.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142020
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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