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- EMDB-48279: cryo-EM map of a full-length and internally HIS-tagged yeast E3 u... -

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Basic information

Entry
Database: EMDB / ID: EMD-48279
Titlecryo-EM map of a full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p construct in an intermediate-open conformation state
Map dataCryo-EM unsharpened map of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an intermediate-conformation state.
Sample
  • Complex: Yeast E3 ubiquitin ligase Tom1p
    • Other: Tom1p (HUWE1)
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: 7.79 Å
AuthorsMadrigal JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170856 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 11, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48279.png

Downloads & links

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Map

FileDownload / File: emd_48279.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 intermediate-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: 0.07
Minimum - Maximum-0.15659082 - 0.5794211
Average (Standard dev.)0.0010018612 (±0.024302037)
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_48279_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...

Fileemd_48279_half_map_1.map
AnnotationCryo-EM half map A of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an intermediate-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...

Fileemd_48279_half_map_2.map
AnnotationCryo-EM half map B of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in an intermediate-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 : Yeast E3 ubiquitin ligase Tom1p

EntireName: Yeast E3 ubiquitin ligase Tom1p
Components
  • Complex: Yeast E3 ubiquitin ligase Tom1p
    • Other: Tom1p (HUWE1)

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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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 377 KDa

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Macromolecule #1: Tom1p (HUWE1)

MacromoleculeName: Tom1p (HUWE1) / type: other / ID: 1
Details: Internal tag insertion between 1074-1075 of the native sequence: SGGGGGGSRHHHHHHHHHHHH
Classification: other
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR MDGLLLKVAE KYKYKQDPKK ECEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN IFGDHNLRKK ...String:
MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR MDGLLLKVAE KYKYKQDPKK ECEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN IFGDHNLRKK TLKLALSLSS SVMDEDGEHF SLVDLYFDKK KVPQKWRKLR FTHYTSNDFK KSSQQKNNIN ETQTSIKKVT MTTQELCEHS LQQIFDKGMA LLPAESWFDF SIKASVAKAF SDDSGENIDL RNIIIETKLN AIAFVNTIFS PPQVSSKLFE LDPYAFNSLT DLISLSETKI PKELRTDALF TLECISLKHV WCSDIIRNLG GNISHGLLFQ ILRYIAKTLR EATDEIDEEY NVRFFYLISN LADVKPLHES LFAAGLIPTL LEIVSIRNCP YKRTLASATH LLETFIDNSE TTTEFIENDG FTMLITSVAN EIDFTLAHPE TWQPPKYSVV YYSISFRELA YIRSLLKLVL KLLSTDSGDR IRNLIDSPIL VSLKKILENK LVFGLTLITY TLDVVQKVIN SEPTIYPVLV EAGLIPYVID NFPKLIGPSA ELLSLLPDVV SAICLNPEGL KQVKEKGLIN NLFDFLLDAD HARILTGGDR STEYGTDIDE LARHYPDLKA NIVEALCNVI RKMPSTFRNE REFLFTSPKD QKYFFHRKNE EILTDKEEHE PAYWELLDKG TMLDTFTSVL FGMSLGNGSF SQVPQHLEAR DFLAIIFMEN PPYEYFTSVA ISNVTEVLQY LDEKYEDYAF MDVMKVLNDQ LENLNDFLNS PNDRSFFLER DGENSVRSCH SKLCRLAAIL NIVTNVYIDL TTLSCKRIMQ IYSYFDKRGF SLIKNLKLLF QKCALEEMYI RQHMPDSVIT ETMPLPIVDV SGDGPPLQIY IDDPKKGDQK GKITSVKTRN TLQMRTILYT LQSNTAILFR CFLRLSHSRN MDLEHKDLTT EVHIFENVVE NVIEMLKATE LEGHLPYILV LLNFNTFVFT IPKASPNSTE ILQTIPAYIF YQKGGYLLYL HIIRDLFTRM TKIKSGGGGG GSRHHHHHHH HHHHHDLSSL DNINYIDESN GILTLSCLIN ALTFYNKSMQ TETMENVQSI GKYYVSIDDD YNIMKALTVP IKVMALAMIL DLDKSDSLFK TQSRNVPYSV FKQLLSMLKN IFTNVNIYTK ELYELHWDLI FPPIKKISLF EQVGIPGDVA ANYLTDTGDD LPADNSIGLF SPEQWEKYKK LIGEDKSIYY PQPMQAQYYK GCSSKELDEL RDTFFNDGLP SRIFTVLPFY PKLVNAFAKT LLQIFTKYDE PTEVFAGRIL DRILETDLDD PATLSSLIHL FGIFLNEKYI YQKASHLMQR FIEYLEKSLK PEHVNTPWFS KALYVYEIIL AKSELPHLEE LSKDVLLRYP LLSMAKVFRI PDPMKQKLFD ILIRVSDISN FYSALATSRI LIFYSRDELY ANNIARSGIL SRLLKVIGSF QKLDKINFLE SSFLLLTRRC FETTENVDAL IRAEINRSFT ARPLGGGDDA VRELTTILEE KAHVVMRSPS QFIDVLCETA RFHEFDDQGA LVDYSLKRFL GEKDKNTQAS STEKSDIYER TGIMHLLLSQ LMAASEKDWL SEPANSSDLP ENKKAQLDPS RNPVCAYMIF LLKLLVELVS SYNQCKFEFL TFSRRNTYAE RPRPRTTAIN FFLYRLLDKP VGTDHDKHEA KRREVIGMLA RSVIIGFLAT VQDDRTTKTD VKLADPHMNF IRKFAIEAII KAIRNATSSS KLLESNHLKL DMWFRIITSM VYVQAPYLRQ LLDSNKVEAD QYQLCKLVID LGLPSVITEA MASIDLNYPF SKKIFNVAVE ALNTISSTRN NFSEHFKIED HDEVEDEVDE SDKEEIPDMF KNSALGMYDV EDIEEDDDDD TSLIGDDDAM AFVDSDNGFE VVFSDEDDDM GEEDADDARS DSEENELSSE MQSSTADGTD VDYEVDDADG LIINIDQPSG DDEEMADYDA NISHSSHSEN EDDASMDVIE VYDDELSSGY DVDLSDYDVD ESDWDSGLSS LSISDEDSES SEDEPINSTR MGDSRRRWLI AEGVELTDDS QGESEEDDRG VFRGIEHIFS NENEPLFRVH DEMRHRNHHR SINRTHFHSA MSAPSLSLLN RGRRNQSNLI NPLGPTGLEQ VENDISDQVT VAGSGSRPRS HHLHFSEVLV SGSFFDEPVL DGIILKSTVS RWKDIFDMFY DSKTYANCII PTVINRLYKV SLALQKDLEN KREQEKLKNK NLLFNEAKVE SHNSSDAISV EQDDIQESNV THDDHEPVYV TIQGSEVDIG GTDIDPEFMN ALPDDIRADV FAQHVRERRA EARLNSDHNV HSREIDSDFL EAIPEDIREG ILDTEAEEQR MFGRIGSSAD VIRADDDVSN NDEEVENGLD HGNSNDRNNA DPEKKKPARI YFAPLIDRAG IASLMKSVFI SKPYIQREIY HELFYRLCSS KQNRNDLMNT FLFILSEGII DQHSLEKVYN IISSRAMGHA KTTTVRQLPS DCTPLTVANQ TIEILQSLID ADSRLKYFLI AEHDNLIVNK ANNKSRKEAL PDKKLRWPLW HLFSLLDRKL ITDESVLMDL LTRILQVCTK TLAVLSTSSN GKENLSKKFH LPSFDEDDLM KILSIIMLDS CTTRVFQQTL NIIYNLSKLQ GCMSIFTKHL VSLAISIMSK LKSALDGLSR EVGTITTGME INSELLQKFT LPSSDQAKLL KILTTVDFLY THKRKEEERN VKDLQSLYDK MNGGPVWSSL SECLSQFEKS QAINTSATIL LPLIESLMVV CRRSDLSQNR NTAVKYEDAK LLDFSKTRVE NLFFPFTDAH KKLLNQMIRS NPKLMSGPFA LLVKNPKVLD FDNKRYFFNA KLKSDNQERP KLPITVRREQ VFLDSYRALF FKTNDEIKNS KLEITFKGES GVDAGGVTRE WYQVLSRQMF NPDYALFLPV PSDKTTFHPN RTSGINPEHL SFFKFIGMII GKAIRDQCFL DCHFSREVYK NILGRPVSLK DMESLDPDYY KSLVWILEND ITDIIEETFS VETDDYGEHK VINLIEGGKD IIVTEANKQD YVKKVVEYKL QTSVKEQMDN FLVGFYALIS KDLITIFDEQ ELELLISGLP DIDVDDWKNN TTYVNYTATC KEVSYFWRAV RSFDAEERAK LLQFVTGTSK VPLNGFKELS GVNGVCKFSI HRDFGSSERL PSSHTCFNQL NLPPYESYET LRGSLLLAIN EGHEGFGLA

UniProtKB: E3 ubiquitin-protein ligase TOM1
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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
VitrificationCryogen name: ETHANE

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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. The selected 41,253 particles were assessed for ab initio reconstruction in 4 classes. NU-refinement was performed on 2 of these classes to give an intermediate-conformation map at 7.79 A resolution from 12,397 particles and an open-conformation map at 7.10 A from 16,098 particles.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12397
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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