GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module

2025-06-18 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name PDBj PDBj 2022-02-08 2022-06-08 2022-06-08 2025-06-18 Max Planck Society Germany GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module Qiao S Cheng JD Schulman BA E3 ubiquitin Ligase, beta-propellor, LIGASE Qiao S Lee CW Sherpa D Chrustowicz J Cheng J Duennebacke M Steigenberger B Karayel O Vu DT von Gronau S Mann M Wilfling F Schulman BA Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation. Nat Commun UK 13 3041 3041 2022 35650207 doi:10.1038/s41467-022-30803-9 2041-1723 Sherpa D Chrustowicz J Qiao S Langlois CR Hehl LA Gottemukkala KV Hansen FM Karayel O von Gronau S Prabu JR Mann M Alpi AF Schulman BA GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme Mol Cell US 81 2445 2459.e13 2021 doi:10.1016/j.molcel.2021.03.025 1097-4164 2168 MOCEFL 7wug FULLOVERLAP Gid12-SRS Gid12-SRS 0 1 2 3 4 5 Saccharomyces cerevisiae 0.392 Vacuolar import and degradation protein 28 Saccharomyces cerevisiae YJM1133 ATCC 204508 / S288c 0.10565820299999999 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MTVAYSLENLKKISNSLVGDQLAKVDYFLAPKCQIFQCLLSIEQSDGVELKNAKLDLLYTLLHLEPQQRDIVGTYYFDIV SAIYKSMSLASSFTKNNSSTNYKYIKLLNLCAGVYPNCGFPDLQYLQNGFIQLVNHKFLRSKCKIDEVVTIIELLKLFLL VDEKNCSDFNKSKFMEEEREVTETSHYQDFKMAESLEHIIVKISSKYLDQISLKYIVRLKVSRPASPSSVKNDPFDNKGV DCTRAIPKKINISNMYDSSLLSLALLLYLRYHYMIPGDRKLRNDATFKMFVLGLLKSNDVNIRCVALKFLLQPYFTEDKK WEDTRTLEKILPYLVKSFNYDPLPWWFDPFDMLDSLIVLYNEITPMNNPVLTTLAHTNVIFCILSRFAQCLSLPQHNEAT LKTTTKFIKICASFAASDEKYRLLLLNDTLLLNHLEYGLESHITLIQDFISLKDEIKETTTESHSMCLPPIYDHDFVAAW LLLLKSFSRSVSALRTTLKRNKIAQLLLQILSKTYTLTKECYFAGQDFMKPEIMIMGITLGSICNFVVEFSNLQSFMLRN GIIDIIEKMLTDPLFNSKKAWDDNEDERRIALQGIPVHEVKANSLWVLRHLMYNCQNEEKFQLLAKIPMNLILDFINDPC WAVQAQCFQLLRNLTCNSRKIVNILLEKFKDVEYKIDPQTGNKISIGSTYLFEFLAKKMRLLNPLDTQQKKAMEGILYII VNLAAVNENKKQLVIEQDEILNIMSEILVETTTDSSSYGNDSNLKLACLWVLNNLLWNSSVSHYTQYAIENGLEPGHSPS DSENPQSTVTIGYNESVAGGYSRGKYYDEPDGDDSSSNANDDEDDDNDEGDDEGDEFVRTPAAKGSTSNVQVTRATVERC RKLVEVGLYDLVRKNITDESLSVREKARTLLYHMDLLLKVK P40547 Glucose-induced degradation protein 8 Saccharomyces cerevisiae ATCC 204508 / S288c 0.051789152 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MTISTLSNETTKSGSCSGQGKNGGKDFTYGKKCFTKEEWKEQVAKYSAMGELYANKTIHYPLKIQPNSSGGSQDEGFATI QTTPIEPTLPRLLLNYFVSMAYEDSSIRMAKELGFIRNNKDIAVFNDLYKIKERFHIKHLIKLGRINEAMEEINSIFGLE VLEETFNATGSYTGRTDRQQQQQQQQFDIDGDLHFKLLLLNLIEMIRSHHQQENITKDSNDFILNLIQYSQNKLAIKASS SVKKMQELELAMTLLLFPLSDSADSGSIKLPKSLQNLYSISLRSKIADLVNEKLLKFIHPRIQFEISNNNSKFPDLLNSD KKIITQNFTVYNNNLVNGSNGTKITHISSDQPINEKMSSNEVTAAANSVWLNQRDGNVGTGSAATTFHNLENKNYWNQTS ELLSSSNGKEKGLEFNNYYSSEFPYEPRLTQIMKLWCWCENQLHHNQIGVPRVEN P40208 Vacuolar import and degradation protein 30 Saccharomyces cerevisiae 0.10828767999999998 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MSEYMDDVDREFINCLFPSYLLQQPVAYDLWILYLQHRKLFHKLKNTNLINADENPTGVGMGRTKLTALTRKEIWSKLMN LGVLGTISFEAVNDDYLIQVYKYFYPDVNDFTLRFGVKDSNKNSVRVMKASSDMRKNAQELLEPVLSEREMALNSNTSLE NDRNDDDDDDDDDDDDDDDDDDDDDESDLESLEGEVDTDTDDNNEGDGSDNHEEGGEEGSRGADADVSSAQQRAERVADP WIYQRSRSAINIETESRNLWDTSDKNSGLQYYPPDQSPSSSFSSPRVSSGNDKNDNEATNVLSNSGSKKKNSMIPDIYKI LGYFLPSRWQAQPNNSLQLSQDGITHLQPNPDYHSYMTYERSSASSASTRNRLRTSFENSGKVDFAVTWANKSLPDNKLT IFYYEIKVLSVTSTESAENSNIVIGYKLVENELMEATTKKSVSRSSVAGSSSSLGGSNNMSSNRVPSTSFTMEGTQRRDY IYEGGVSAMSLNVDGSINKCQKYGFDLNVFGYCGFDGLITNSTEQSKEYAKPFGRDDVIGCGINFIDGSIFFTKNGIHLG NAFTDLNDLEFVPYVALRPGNSIKTNFGLNEDFVFDIIGYQDKWKSLAYEHICRGRQMDVSIEEFDSDESEEDETENGPE ENKSTNVNEDLMDIDQEDGAAGNKDTKKLNDEKDNNLKFLLGEDNRFIDGKLVRPDVNNINNLSVDDGSLPNTLNVMIND YLIHEGLVDVAKGFLKDLQKDAVNVNGQHSESKDVIRHNERQIMKEERMVKIRQELRYLINKGQISKCINYIDNEIPDLL KNNLELVFELKLANYLVMIKKSSSKDDDEIENLILKGQELSNEFIYDTKIPQSLRDRFSGQLSNVSALLAYSNPLVEAPK EISGYLSDEYLQERLFQVSNNTILTFLHKDSECALENVISNTRAMLSTLLEYNAFGSTNSSDPRYYKAINFDEDVLNL A0A6L0ZCH7 Vacuolar import and degradation protein 24 Saccharomyces cerevisiae 0.041291934 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MINNPKVDSVAEKPKAVTSKQSEQAASPEPTPAPPVSRNQYPITFNLTSTAPFHLHDRHRYLQEQDLYKCASRDSLSSLQ QLAHTPNGSTRKKYIVEDQSPYSSENPVIVTSSYNHTVCTNYLRPRMQFTGYQISGYKRYQVTVNLKTVDLPKKDCTSLS PHLSGFLSIRGLTNQHPEISTYFEAYAVNHKELGFLSSSWKDEPVLNEFKATDQTDLEHWINFPSFRQLFLMSQKNGLNS TDDNGTTNAAKKLPPQQLPTTPSADAGNISRIFSQEKQFDNYLNERFIFMKWKEKFLVPDALLMEGVDGASYDGFYYIVH DQVTGNIQGFYYHQDAEKFQQLELVPSLKNKVESSDCSFEFA A0A6A5Q1W0 HLJ1_G0042170.mRNA.1.CDS.1 Saccharomyces cerevisiae 0.08156457799999998 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MATGRIQFAVSTPCNTKGKPSGYRLFEFKNDRLALVPSERGCTKVDVNANIQAFCYLRPNGRDTSISPDATHILDSCDYM VLAKSNGFIEIISNYQYKIKNGLRLAPSYILRCTPEDFESNFFSDYMIAGLEYSQGLLYCCMCSGRIYVFVMNLPTDYIQ YKNMYNPMFPDCFFKVHHDNNTTHSSEEEKLFEGSTRYTGRSCSKHICYFLLPIEPSHLRSSPVVSSFCNMYQGLPIYRP SMYLHIERGISTFHINPLDRFCFMTVSPRSPLFIRKIILPLTYVTFLSTFISLKNSIQGDTCGEILSWDNVAQQNGFGSL FSWISNKFTFDTDIINSTIWDDIVKYSGTGMLDSGIVWKQRQGHAKDDIYELFHTQDMLGSSRRNSSFSTASSEPRPLSR RRRESFQALTRDAFRERMDVPCSTKWELDSFIRGLRRNTFMVDFEIVEKISHRNGNDGVNEDDNTTDESDETMTSFLTDN YKKMDIVCIDHFVTLSAFRPRYYDEPIIKIDSLSNKNGSENGTNEEEWAESQMKVDGQVIDDETAQFKQALGNLCSFKKL FMLDDSLCFILDTHGVLLINRFEIKNTKNLLRNSKDTIRIIPHDFGLINDTIVIINDIDVGTDNVCALTFHLVVTSMAGE ITVLKGEFFKNCRLGRIKLCDSLKLNRKDRFVDKLALIDYDGLNAQKRRLDYDEKDLYTFIVKKVKRD A0A6A5Q188 singleParticle particle 0.25 6.5

25mM MES pH6.5 + 500mM NaCl + 1mM DTT

C-flat-1.2/1.3 COPPER 200 GLOW DISCHARGE 30 ETHANE 100 39 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1.335 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

initial model generated by Relion GUI

1 C1 FOURIER SPACE 3.3 FSC 0.143 CUT-OFF 198503 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 3 8023.0 emd_32830.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 305.2 305.2 305.2 90.0 90.0 90.0 X Y Z -0.12282244 0.22567104 0.00032438835 0.005100165 1.09 1.09 1.09 0.0445 AUTHOR ::::EMDATABANK.org::::EMD-32830::::