Substrate receptor scaffolding module of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to Fbp1 substrate

2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DERIVED_CALCULATIONS pdbx_struct_sheet_hbond struct_sheet struct_sheet_order struct_sheet_range _struct_sheet.id _struct_sheet.number_strands DERIVED_CALCULATIONS struct_conf DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first COORDINATE_REPLACEMENT AUTHOR Model completeness

We made a residue shift in a beta sheet starting residue K338 - L348 in the chain 4 (protein-Gid4)

REFINEMENT_DESCRIPTION atom_site atom_site_anisotrop em_software pdbx_struct_assembly_prop pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact pdbx_validate_torsion refine_ls_restr struct_conn _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.id _atom_site_anisotrop.pdbx_auth_asym_id _atom_site_anisotrop.pdbx_auth_atom_id _atom_site_anisotrop.pdbx_auth_comp_id _atom_site_anisotrop.pdbx_auth_seq_id _atom_site_anisotrop.pdbx_label_asym_id _atom_site_anisotrop.pdbx_label_atom_id _atom_site_anisotrop.pdbx_label_comp_id _atom_site_anisotrop.pdbx_label_seq_id _atom_site_anisotrop.type_symbol _em_software.category _em_software.fitting_id _em_software.imaging_id _pdbx_struct_assembly_prop.value _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _refine_ls_restr.dev_ideal _refine_ls_restr.number _struct_conn.pdbx_dist_value STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond citation database_2 em_admin pdbx_entry_details pdbx_modification_feature _citation.journal_id_ISSN _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2021-03-05 2021-05-05 2021-05-05 2025-07-09 European Research Council (ERC) 789016-NEDD8Activate Germany German Research Foundation (DFG) SCHU 3196/1-1 Germany Substrate receptor scaffolding module of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to Fbp1 substrate Sherpa D Chrustowicz J Prabu JR Schulman BA GID, CTLH, ubiquitin, E3 ligase, supramolecular assembly, metabolism, gluconeogenesis, cryoEM, LIGASE 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 2021 33905682 doi:10.1016/j.molcel.2021.03.025 1097-2765 2168 MOCEFL Sherpa D Chrustowicz J Qiao S Langlois CR Hehl LA Gottemukkala KV Hansen FM Karayel O Prabu JR Mann M Alpi AF Schulman BA GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme Biorxiv US 2021 doi:10.1101/2021.04.07.436316 2692-8205 EMD-12541 other EM volume

Structure of Apo Chelator-GID SR4

EMD-12557 other EM volume

Structure of Chelator-GID SR4 bound to Fbp1

EMD-12548 other EM volume

Structure of GID SR4

EMD-12538 other EM volume

Structure of endogenous GID Ant

EMD-12540 other EM volume

Structure of endogenous Chelator-GID Ant

7ns3 FULLOVERLAP Substrate receptor scaffolding module of yeast Chelator-GID SR4 comprising Gid1, Gid4, Gid5, Gid8 and Gid9 bound to Fbp1 Substrate receptor scaffolding module of yeast Chelator-GID SR4 comprising Gid1, Gid4, Gid5, Gid8 and Gid9 bound to Fbp1 0 1 2 3 4 5 6

Generated by focused refinement of Chelator-GID SR4 + Fbp1 map

Saccharomyces cerevisiae 0.31 Vacuolar import and degradation protein 28 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.105609133 1 Trichoplusia ni LEVO MTVAYSLENLKKISNSLVGDQLAKVDYFLAPKCQIFQCLLSIEQSDGVELKNAKLDLLYTLLHLEPQQRDIVGTYYFDIV SAIYKSMSLASSFTKNNSSTNYKYIKLLNLCAGVYPNCGFPDLQYLQNGFIQLVNHKFLRSKCKIDEVVTIIELLKLFLL VDEKNCSDFNKSKFMEEEREVTETSHYQDFKMAESLEHIIVKISSKYLDQISLKYIVRLKVSRPASPSSVKNDPFDNKGV DCTRAIPKKINISNMYDSSLLSLALLLYLRYHYMIPGDRKLRNDATFKMFVLGLLKSNDVNIRCVALKFLLQPYFTEDKK WEDTRTLEKILPYLVKSFNYDPLPWWFDPFDMLDSLIVLYNEITPMNNPVLTTLAHTNVIFCILSRFAQCLSLPQHNEAT LKTTTKFIKICASFAASDEKYRLLLLNDTLLLNHLEYGLESHITLIQDFISLKDEIKETTTESHSMCLPPIYDHDFVAAW LLLLKSFSRSVSALRTTLKRNKIAQLLLQILSKTYTLTKECYFAGQDFMKPEIMIMGITLGSICNFVVEFSNLQSFMLRN GIIDIIEKMLTDPLFNSKKAWDDNEDERRIALQGIPVHEVKANSLWVLRHLMYNCQNEEKFQLLAKIPMNLILDFINDPC WAVQAQCFQLLRNLTCNSRKIVNILLEKFKDVEYKIDPQTGNKISIGSTYLFEFLAKKMRLLNPLDTQQKKAMEGILYII VNLAAVNENKKQLVIEQDEILNIMSEILVETTTDSSSNGNDSNLKLACLWVLNNLLWNSSVSHYTQYAIENGLEPGHSPS DSENPQSTVTIGYNESVAGGYSRGKYYDEPDGDDSSSNANDDEDDDNDEGDDEGDEFVRTPAAKGSTSNVQVTRATVERC RKLVEVGLYDLVRKNITDESLSVREKARTLLYHMDLLLKVK P40547 Glucose-induced degradation protein 8 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.055803308999999995 1 Trichoplusia ni LEVO MTISTLSNETTKSGSCSGQGKNGGKDFTYGKKCFTKEEWKEQVAKYSAMGELYANKTIHYPLKIQPNSSGGSQDEGFATI QTTPIEPTLPRLLLNYFVSMAYEDSSIRMAKELGFIRNNKDIAVFNDLYKIKERFHIKHLIKLGRINEAMEEINSIFGLE VLEETFNATGSYTGRTDRQQQQQQQQFDIDGDLHFKLLLLNLIEMIRSHHQQENITKDSNDFILNLIQYSQNKLAIKASS SVKKMQELELAMTLLLFPLSDSADSGSIKLPKSLQNLYSISLRSKIADLVNEKLLKFIHPRIQFEISNNNSKFPDLLNSD KKIITQNFTVYNNNLVNGSNGTKITHISSDQPINEKMSSNEVTAAANSVWLNQRDGNVGTGSAATTFHNLENKNYWNQTS ELLSSSNGKEKGLEFNNYYSSEFPYEPRLTQIMKLWCWCENQLHHNQIGVPRVENSDENLYFQSGWSHPQFEKGGGSGGG SGGSAWSHPQFEK P40208 BJ4_G0018240.mRNA.1.CDS.1 Saccharomyces cerevisiae 0.10828767999999998 1 Trichoplusia ni LEVO MSEYMDDVDREFINCLFPSYLLQQPVAYDLWILYLQHRKLFHKLKNTNLINADENPTGVGMGRTKLTALTRKEIWSKLMN LGVLGTISFEAVNDDYLIQVYKYFYPDVNDFTLRFGVKDSNKNSVRVMKASSDMRKNAQELLEPVLSEREMALNSNTSLE NDRNDDDDDDDDDDDDDDDDDDDDDESDLESLEGEVDTDTDDNNEGDGSDNHEEGGEEGSRGADADVSSAQQRAERVADP WIYQRSRSAINIETESRNLWDTSDKNSGLQYYPPDQSPSSSFSSPRVSSGNDKNDNEATNVLSNSGSKKKNSMIPDIYKI LGYFLPSRWQAQPNNSLQLSQDGITHLQPNPDYHSYMTYERSSASSASTRNRLRTSFENSGKVDFAVTWANKSLPDNKLT IFYYEIKVLSVTSTESAENSNIVIGYKLVENELMEATTKKSVSRSSVAGSSSSLGGSNNMSSNRVPSTSFTMEGTQRRDY IYEGGVSAMSLNVDGSINKCQKYGFDLNVFGYCGFDGLITNSTEQSKEYAKPFGRDDVIGCGINFIDGSIFFTKNGIHLG NAFTDLNDLEFVPYVALRPGNSIKTNFGLNEDFVFDIIGYQDKWKSLAYEHICRGRQMDVSIEEFDSDESEEDETENGPE ENKSTNVNEDLMDIDQEDGAAGNKDTKKLNDEKDNNLKFLLGEDNRFIDGKLVRPDVNNINNLSVDDGSLPNTLNVMIND YLIHEGLVDVAKGFLKDLQKDAVNVNGQHSESKDVIRHNERQIMKEERMVKIRQELRYLINKGQISKCINYIDNEIPDLL KNNLELVFELKLANYLVMIKKSSSKDDDEIENLILKGQELSNEFIYDTKIPQSLRDRFSGQLSNVSALLAYSNPLVEAPK EISGYLSDEYLQERLFQVSNNTILTFLHKDSECALENVISNTRAMLSTLLEYNAFGSTNSSDPRYYKAINFDEDVLNL A0A6L0ZCH7 Protein FYV10 Saccharomyces cerevisiae 0.059975101999999995 1 Trichoplusia ni LEVO MAEKSIFNEPDVDFHLKLNQQLFHIPYELLSKRIKHTQAVINKETKSLHEHTAALNQIFEHNDVEHDELALAKITEMIRK VDHIERFLNTQIKSYCQILNRIKKRLEFFHELKDIKSQNSGTSHNGNNEGTRTKLIQWYQSYTNILIGDYLTRNNPIKYN SETKDHWNSGVVFLKQSQLDDLIDYDVLLEANRISTSLLHERNLLPLISWINENKKTLTKKSSILEFQARLQEYIELLKV DNYTDAIVCFQRFLLPFVKSNFTDLKLASGLLIFIKYCNDQKPTSSTSSGFDTEEIKSQSLPMKKDRIFQHFFHKSLPRI TSKPAVNTTDYDKSSLINLQSGDFERYLNLLDDQRWSVLNDLFLSDFYSMYGISQNDPLLIYLSLGISSLKTRDCLHPSD DENGNQETETATTAEKEVEDLQLFTLHSLKRKNCPVCSETFKPITQALPFAHHIQSQLFENPILLPNGNVYDSKKLKKLA KTLKKQNLISLNPGQIMDPVDMKIFCESDSIKMYPT A0A6A5PZU1 Vacuolar import and degradation protein 24 Saccharomyces cerevisiae 0.041291934 1 Escherichia coli LEVO MINNPKVDSVAEKPKAVTSKQSEQAASPEPTPAPPVSRNQYPITFNLTSTAPFHLHDRHRYLQEQDLYKCASRDSLSSLQ QLAHTPNGSTRKKYIVEDQSPYSSENPVIVTSSYNHTVCTNYLRPRMQFTGYQISGYKRYQVTVNLKTVDLPKKDCTSLS PHLSGFLSIRGLTNQHPEISTYFEAYAVNHKELGFLSSSWKDEPVLNEFKATDQTDLEHWINFPSFRQLFLMSQKNGLNS TDDNGTTNAAKKLPPQQLPTTPSADAGNISRIFSQEKQFDNYLNERFIFMKWKEKFLVPDALLMEGVDGASYDGFYYIVH DQVTGNIQGFYYHQDAEKFQQLELVPSLKNKVESSDCSFEFA A0A6A5Q1W0 Fructose-bisphosphatase Saccharomyces cerevisiae 0.038303473 1 Escherichia coli LEVO MPTLVNGPRRDSTEGFDTDIITLPRFIIEHQKQFKNATGDFTLVLNALQFAFKFVSHTIRRAELVNLVGLAGASNFTGDQ QKKLDVLGDEIFINAMRASGIIKVLVSEEQEDLIVFPTNTGSYAVCCDPIDGSSNLDAGVSVGTIASIFRLLPDSSGTIN DVLRCGKEMVAACYAMYGSSTHLVLTLGDGVDGFTLDTNLGEFILTHPNLRIPPQKAIYSINEGNTLYWNETIRTFIEKV KQPQADNNNKPFSARYVGSMVADVHRTFLYGGLFAYPCDKKSPNGKLRLLYEAFPMAFLMEQAGGKAVNDRGERILDLVP SHIHDKSSIWLGSSGEIDKFLDHIGKSQ A0A6A5PV82 3.1.3.11 singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 BIOQUANTUM (6k x 4k) 79.2 1 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-12557 3.5 FSC 0.143 CUT-OFF 74929 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_12559.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 455.04 455.04 455.04 90.0 90.0 90.0 X Y Z -0.09341251 0.20251693 0.00016793663 0.0032407593 1.58 1.58 1.58 0.045 AUTHOR ::::EMDATABANK.org::::EMD-12559:::: emd_12559_msk_1.map emd_12559_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 455.04 455.04 455.04 90.0 90.0 90.0 X Y Z -0.035760578 0.113230556 0.00014684528 0.0037638398 1.58 1.58 1.58 AUTHOR ::::EMDATABANK.org::::EMD-12559:::: emd_12559_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 455.04 455.04 455.04 90.0 90.0 90.0 X Y Z -0.03036901 0.12018819 0.00018746518 0.0037631723 1.58 1.58 1.58 AUTHOR ::::EMDATABANK.org::::EMD-12559::::