2026-04-22 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES em_admin pdbx_database_related _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin pdbx_database_related _em_admin.last_update RCSB RCSB 2024-11-21 2025-10-01 2025-10-01 2026-04-22 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 E3 ubiquitin ligase HUWE1 homolog Tom1p in closed-conformation with internal Acidic Domain deletion. Madrigal JM alpha solenoid, E3 ubiquitin ligase, stress response, cell-cycle, GENE REGULATION Madrigal J Schubert HL Sdano MA McCullough L Connell Z Formosa T Hill CP Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters Elife US 2024 doi:10.7554/elife.101393.1 2050-084X 9egk FULLOVERLAP EMDB EMD-47989 associated EM volume
E3 ubiquitin ligase HUWE1 homolog Tom1p in closed-conformation with internal Acidic Domain deletion.
 PDB 9CMR unspecified PDB 9ELD unspecified PDB 9MHP unspecified Yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain (residues 1873-2131). Yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain (residues 1873-2131). 0 1
C-terminally tagged with Protein A for purification, cleaved with Prescission Protease.
Saccharomyces cerevisiae E3 ubiquitin-protein ligase TOM1 Saccharomyces cerevisiae 0.375512594
E1873-E2131 deleted in construct Precission Protease tag appended to C-terminus
1 Saccharomyces cerevisiae LEVO MVLFTRCEKARKEKLAAGYKPLVDYLIDCDTPTFLERIEAIQEWDRSRDDLYVWIPILDRMDGLLLKVAEKYKYKQDPKK ECEVKLVEMEAHDVDYCLKMLKFTRRLLLNTENRFVYSSGDVLMYLLNCPNFTIKLAVMRILAILGERFVIAREKIVAHN IFGDHNLRKKTLKLALSLSSSVMDEDGEHFSLVDLYFDKKKVPQKWRKLRFTHYTSNDFKKSSQQKNNINETQTSIKKVT MTTQELCEHSLQQIFDKGMALLPAESWFDFSIKASVAKAFSDDSGENIDLRNIIIETKLNAIAFVNTIFSPPQVSSKLFE LDPYAFNSLTDLISLSETKIPKELRTDALFTLECISLKHVWCSDIIRNLGGNISHGLLFQILRYIAKTLREATDEIDEEY NVRFFYLISNLADVKPLHESLFAAGLIPTLLEIVSIRNCPYKRTLASATHLLETFIDNSETTTEFIENDGFTMLITSVAN EIDFTLAHPETWQPPKYSVVYYSISFRELAYIRSLLKLVLKLLSTDSGDRIRNLIDSPILVSLKKILENKLVFGLTLITY TLDVVQKVINSEPTIYPVLVEAGLIPYVIDNFPKLIGPSAELLSLLPDVVSAICLNPEGLKQVKEKGLINNLFDFLLDAD HARILTGGDRSTEYGTDIDELARHYPDLKANIVEALCNVIRKMPSTFRNEREFLFTSPKDQKYFFHRKNEEILTDKEEHE PAYWELLDKGTMLDTFTSVLFGMSLGNGSFSQVPQHLEARDFLAIIFMENPPYEYFTSVAISNVTEVLQYLDEKYEDYAF MDVMKVLNDQLENLNDFLNSPNDRSFFLERDGENSVRSCHSKLCRLAAILNIVTNVYIDLTTLSCKRIMQIYSYFDKRGF SLIKNLKLLFQKCALEEMYIRQHMPDSVITETMPLPIVDVSGDGPPLQIYIDDPKKGDQKGKITSVKTRNTLQMRTILYT LQSNTAILFRCFLRLSHSRNMDLEHKDLTTEVHIFENVVENVIEMLKATELEGHLPYILVLLNFNTFVFTIPKASPNSTE ILQTIPAYIFYQKGGYLLYLHIIRDLFTRMTKIKDLSSLDNINYIDESNGILTLSCLINALTFYNKSMQTETMENVQSIG KYYVSIDDDYNIMKALTVPIKVMALAMILDLDKSDSLFKTQSRNVPYSVFKQLLSMLKNIFTNVNIYTKELYELHWDLIF PPIKKISLFEQVGIPGDVAANYLTDTGDDLPADNSIGLFSPEQWEKYKKLIGEDKSIYYPQPMQAQYYKGCSSKELDELR DTFFNDGLPSRIFTVLPFYPKLVNAFAKTLLQIFTKYDEPTEVFAGRILDRILETDLDDPATLSSLIHLFGIFLNEKYIY QKASHLMQRFIEYLEKSLKPEHVNTPWFSKALYVYEIILAKSELPHLEELSKDVLLRYPLLSMAKVFRIPDPMKQKLFDI LIRVSDISNFYSALATSRILIFYSRDELYANNIARSGILSRLLKVIGSFQKLDKINFLESSFLLLTRRCFETTENVDALI RAEINRSFTARPLGGGDDAVRELTTILEEKAHVVMRSPSQFIDVLCETARFHEFDDQGALVDYSLKRFLGEKDKNTQASS TEKSDIYERTGIMHLLLSQLMAASEKDWLSEPANSSDLPENKKAQLDPSRNPVCAYMIFLLKLLVELVSSYNQCKFEFLT FSRRNTYAERPRPRTTAINFFLYRLLDKPVGTDHDKHEAKRREVIGMLARSVIIGFLATVQDDRTTKTDVKLADPHMNFI RKFAIEAIIKAIRNATSSSKLLESNHLKLDMWFRIITSMVYVQAPYLRQLLDSNKVEADQYQLCKLVIDLGLPSVITEAM ASIDLNYPFSKKIFNVAVEALNTISSTRNNFSEHFKIEDHDEVEDEVDESDKEEIPDMFKNSALGMYDVEDIEEDDDDDT SLIGDDDAMAFVDSDNGFEVVFSDEDDDMGEEDADDARSDSEENELSSEMQSSTADGTDVDYEVDDADGLIINIDQPSGD DEEMADYDANISHSSHSENEDDASMDVIEVYDDELSSGYDVDLSDYDVDESDWDSGLSSLSISDEDSESSEDEPINSTRM GDSRRRWLIAEGVELTDDSQGESEEDDRGVFRGIEHIFSNENEPLFRVHDEMRHRNHHRSINRTHFHSAMSAPSLSLLNR GRRNQSNLINPLGPTGLEQVENDISDQVTVAGSGSRPRSHHLHFSEVLVSGSFFDEPVLDGIILKSTVSRWKDIFDMFYD SKTYANCIIPTVINRLYKVSLALQKDLENKREQEKLKNKNLLFNEAKVESHNSSDAISVEQDDIQESNVTHDDHEPVYVT IQGSEVDIGGTDIDPEFMNALPDDIRADVFAQHVRERRAEARLNSDHNVHSREIDSDFLEAIPEDIREGILDTEAEEQRM FGRIGSSADVIRADDDVSNNDEEVENGLDHGNSNDRNNADPEKKKPARIYFAPLIDRAGIASLMKSVFISKPYIQREIYH ELFYRLCSSKQNRNDLMNTFLFILSEGIIDQHSLEKVYNIISSRAMGHAKTTTVRQLPSDCTPLTVANQTIEILQSLIDA DSRLKYFLIAEHDNLIVNKANNKSRKEALPDKKLRWPLWHLFSLLDRKLITDESVLMDLLTRILQVCTKTLAVLSTSSNG KENLSKKFHLPSFDEDDLMKILSIIMLDSCTTRVFQQTLNIIYNLSKLQGCMSIFTKHLVSLAISIMSKLKSALDGLSRE VGTITTGMEINSELLQKFTLPSSDQAKLLKILTTVDFLYTHKRKEEERNVKDLQSLYDKMNGGPVWSSLSECLSQFEKSQ AINTSATILLPLIESLMVVCRRSDLSQNRNTAVKYEDAKLLDFSKTRVENLFFPFTDAHKKLLNQMIRSNPKLMSGPFAL LVKNPKVLDFDNKRYFFNAKLKSDNQERPKLPITVRREQVFLDSYRALFFKTNDEIKNSKLEITFKGESGVDAGGVTREW YQVLSRQMFNPDYALFLPVPSDKTTFHPNRTSGINPEHLSFFKFIGMIIGKAIRDQCFLDCHFSREVYKNILGRPVSLKD MESLDPDYYKSLVWILENDITDIIEETFSVETDDYGEHKVINLIEGGKDIIVTEANKQDYVKKVVEYKLQTSVKEQMDNF LVGFYALISKDLITIFDEQELELLISGLPDIDVDDWKNNTTYVNYTATCKEVSYFWRAVRSFDAEERAKLLQFVTGTSKV PLNGFKELSGVNGVCKFSIHRDFGSSERLPSSHTCFNQLNLPPYESYETLRGSLLLAINEGHEGFGLALEVLFQGP Q03280 2.3.2.26 singleParticle particle 1 7.0 ETHANE 100 FEI VITROBOT MARK I
Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. The detergent sample was concentrated to 8.1 mg/mL in 0.01% CHAPS and 0.05% NP-40. 2.5 uL of sample was applied to grids and blotted for 2.5 seconds before vitrification by plunging into liquid ethane. For samples without detergent, protein was concentrated to 0.44 mg/mL and blotted for 1.5 seconds before vitrification..
TFS KRIOS FLOOD BEAM OTHER FIELD EMISSION GUN 300 0.8 2.0 GATAN K3 (6k x 4k) 7236 47.0
A total of 2,865 movies were recorded from grids without detergent at 81,000x magnification on a 300 kV Titan Krios G3 electron microscope with a K3 direct detector (nominal resolution after 2x binning is 1.06A/px). Electron exposure was 47 (e-/A2) over a total of 40 frames. A total of 4,371 movies were recorded from with-detergent grids using the same electron microscope and collection parameters.
 1 cryoSPARC NONE
Initial blob auto-picking, 2D classification, ab initio reconstructions and heterogeneous refinements from the non-detergent sample led to 3 refined volumes. Templates were low-pass filtered to 17 A, creating 25 equally spaced templates each for a total of 75 templates. These templates were used to template-pick from both non-detergent and detergent sample datasets.
 3.07 FSC 0.143 CUT-OFF cryoSPARC Non-uniform refinement
The separately processed dataset #1 and #2 particles were combined for a total of 531,549 starting particles for further processing and refinement. A round of 2D classification resulted in selection of 477,889 particles, which were Fourier cropped from a box size of 680 to 320 pixels for further processing. Two-component 3DVA was performed after map refinement of the combined dataset with a filter resolution of 4 A. 3DVA display was subsequently run to give 8 intermediates along the first principal component at a filter resolution of 5 A. The top 4 intermediates with the highest number of particles were combined to yield 462,711 and refined using non-uniform refinement to an estimated overall resolution of 3.07 A.
462711 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD cryoSPARC emd_47989.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 360.39996 360.39996 360.39996 90.0 90.0 90.0 X Y Z -3.4387705 4.8699923 0.0006759767 0.0760753 1.1262499 1.1262499 1.1262499 0.27 AUTHOR Sharpened map of the C-terminally tagged yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain, in closed-conformation with helical repeat solenoid architecture. emd_47989_msk_1.map emd_47989_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 360.39996 360.39996 360.39996 90.0 90.0 90.0 X Y Z -0.5267381 1.2773587 0.0006759767 0.029728444 1.1262499 1.1262499 1.1262499 AUTHOR Unsharpened map of the C-terminally tagged yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain, in closed-conformation with helical repeat solenoid architecture. emd_47989_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 360.39996 360.39996 360.39996 90.0 90.0 90.0 X Y Z -0.57951725 1.3576252 0.0011812433 0.038801108 1.1262499 1.1262499 1.1262499 AUTHOR Cryo-EM half-map A of the C-terminally tagged yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain, in closed-conformation with helical repeat solenoid architecture. emd_47989_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 360.39996 360.39996 360.39996 90.0 90.0 90.0 X Y Z -0.542175 1.4020958 0.0011816118 0.038849887 1.1262499 1.1262499 1.1262499 AUTHOR Cryo-EM half-map B of the C-terminally tagged yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain, in closed-conformation with helical repeat solenoid architecture.