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Yorodumi- EMDB-32830: GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32830 | |||||||||
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Title | GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module | |||||||||
Map data | ||||||||||
Sample |
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Keywords | E3 ubiquitin Ligase / beta-propellor / LIGASE | |||||||||
Function / homology | Function and homology information protein catabolic process in the vacuole / GID complex / Regulation of pyruvate metabolism / ascospore formation / traversing start control point of mitotic cell cycle / vacuole / negative regulation of gluconeogenesis / Neutrophil degranulation / cell cycle / positive regulation of canonical Wnt signaling pathway ...protein catabolic process in the vacuole / GID complex / Regulation of pyruvate metabolism / ascospore formation / traversing start control point of mitotic cell cycle / vacuole / negative regulation of gluconeogenesis / Neutrophil degranulation / cell cycle / positive regulation of canonical Wnt signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae YJM1133 (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Qiao S / Cheng JD / Schulman BA | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation. Authors: Shuai Qiao / Chia-Wei Lee / Dawafuti Sherpa / Jakub Chrustowicz / Jingdong Cheng / Maximilian Duennebacke / Barbara Steigenberger / Ozge Karayel / Duc Tung Vu / Susanne von Gronau / Matthias ...Authors: Shuai Qiao / Chia-Wei Lee / Dawafuti Sherpa / Jakub Chrustowicz / Jingdong Cheng / Maximilian Duennebacke / Barbara Steigenberger / Ozge Karayel / Duc Tung Vu / Susanne von Gronau / Matthias Mann / Florian Wilfling / Brenda A Schulman / Abstract: Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced ...Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1), malate dehydrogenase (Mdh2), and other gluconeogenic enzymes. "GID" is a collection of E3 ligase complexes; a core scaffold, RING-type catalytic core, and a supramolecular assembly module together with interchangeable substrate receptors select targets for ubiquitylation. However, knowledge of additional cellular factors directly regulating GID-type E3s remains rudimentary. Here, we structurally and biochemically characterize Gid12 as a modulator of the GID E3 ligase complex. Our collection of cryo-EM reconstructions shows that Gid12 forms an extensive interface sealing the substrate receptor Gid4 onto the scaffold, and remodeling the degron binding site. Gid12 also sterically blocks a recruited Fbp1 or Mdh2 from the ubiquitylation active sites. Our analysis of the role of Gid12 establishes principles that may more generally underlie E3 ligase regulation. #1: Journal: Mol Cell / Year: 2021 Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme Authors: 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 | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32830.map.gz | 8.6 MB | EMDB map data format | |
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Header (meta data) | emd-32830-v30.xml emd-32830.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
Images | emd_32830.png | 76.3 KB | ||
Filedesc metadata | emd-32830.cif.gz | 8.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32830 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32830 | HTTPS FTP |
-Related structure data
Related structure data | 7wugMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32830.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Gid12-SRS
Entire | Name: Gid12-SRS |
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Components |
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-Supramolecule #1: Gid12-SRS
Supramolecule | Name: Gid12-SRS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 392 KDa |
-Macromolecule #1: Vacuolar import and degradation protein 28
Macromolecule | Name: Vacuolar import and degradation protein 28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae YJM1133 (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 105.658203 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MTVAYSLENL KKISNSLVGD QLAKVDYFLA PKCQIFQCLL SIEQSDGVEL KNAKLDLLYT LLHLEPQQRD IVGTYYFDIV SAIYKSMSL ASSFTKNNSS TNYKYIKLLN LCAGVYPNCG FPDLQYLQNG FIQLVNHKFL RSKCKIDEVV TIIELLKLFL L VDEKNCSD ...String: MTVAYSLENL KKISNSLVGD QLAKVDYFLA PKCQIFQCLL SIEQSDGVEL KNAKLDLLYT LLHLEPQQRD IVGTYYFDIV SAIYKSMSL ASSFTKNNSS TNYKYIKLLN LCAGVYPNCG FPDLQYLQNG FIQLVNHKFL RSKCKIDEVV TIIELLKLFL L VDEKNCSD FNKSKFMEEE REVTETSHYQ DFKMAESLEH IIVKISSKYL DQISLKYIVR LKVSRPASPS SVKNDPFDNK GV DCTRAIP KKINISNMYD SSLLSLALLL YLRYHYMIPG DRKLRNDATF KMFVLGLLKS NDVNIRCVAL KFLLQPYFTE DKK WEDTRT LEKILPYLVK SFNYDPLPWW FDPFDMLDSL IVLYNEITPM NNPVLTTLAH TNVIFCILSR FAQCLSLPQH NEAT LKTTT KFIKICASFA ASDEKYRLLL LNDTLLLNHL EYGLESHITL IQDFISLKDE IKETTTESHS MCLPPIYDHD FVAAW LLLL KSFSRSVSAL RTTLKRNKIA QLLLQILSKT YTLTKECYFA GQDFMKPEIM IMGITLGSIC NFVVEFSNLQ SFMLRN GII DIIEKMLTDP LFNSKKAWDD NEDERRIALQ GIPVHEVKAN SLWVLRHLMY NCQNEEKFQL LAKIPMNLIL DFINDPC WA VQAQCFQLLR NLTCNSRKIV NILLEKFKDV EYKIDPQTGN KISIGSTYLF EFLAKKMRLL NPLDTQQKKA MEGILYII V NLAAVNENKK QLVIEQDEIL NIMSEILVET TTDSSSYGND SNLKLACLWV LNNLLWNSSV SHYTQYAIEN GLEPGHSPS DSENPQSTVT IGYNESVAGG YSRGKYYDEP DGDDSSSNAN DDEDDDNDEG DDEGDEFVRT PAAKGSTSNV QVTRATVERC RKLVEVGLY DLVRKNITDE SLSVREKART LLYHMDLLLK VK UniProtKB: Vacuolar import and degradation protein 28 |
-Macromolecule #2: Glucose-induced degradation protein 8
Macromolecule | Name: Glucose-induced degradation protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 51.789152 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MTISTLSNET TKSGSCSGQG KNGGKDFTYG KKCFTKEEWK EQVAKYSAMG ELYANKTIHY PLKIQPNSSG GSQDEGFATI QTTPIEPTL PRLLLNYFVS MAYEDSSIRM AKELGFIRNN KDIAVFNDLY KIKERFHIKH LIKLGRINEA MEEINSIFGL E VLEETFNA ...String: MTISTLSNET TKSGSCSGQG KNGGKDFTYG KKCFTKEEWK EQVAKYSAMG ELYANKTIHY PLKIQPNSSG GSQDEGFATI QTTPIEPTL PRLLLNYFVS MAYEDSSIRM AKELGFIRNN KDIAVFNDLY KIKERFHIKH LIKLGRINEA MEEINSIFGL E VLEETFNA TGSYTGRTDR QQQQQQQQFD IDGDLHFKLL LLNLIEMIRS HHQQENITKD SNDFILNLIQ YSQNKLAIKA SS SVKKMQE LELAMTLLLF PLSDSADSGS IKLPKSLQNL YSISLRSKIA DLVNEKLLKF IHPRIQFEIS NNNSKFPDLL NSD KKIITQ NFTVYNNNLV NGSNGTKITH ISSDQPINEK MSSNEVTAAA NSVWLNQRDG NVGTGSAATT FHNLENKNYW NQTS ELLSS SNGKEKGLEF NNYYSSEFPY EPRLTQIMKL WCWCENQLHH NQIGVPRVEN UniProtKB: Glucose-induced degradation protein 8 |
-Macromolecule #3: Vacuolar import and degradation protein 30
Macromolecule | Name: Vacuolar import and degradation protein 30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 108.28768 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MSEYMDDVDR EFINCLFPSY LLQQPVAYDL WILYLQHRKL FHKLKNTNLI NADENPTGVG MGRTKLTALT RKEIWSKLMN LGVLGTISF EAVNDDYLIQ VYKYFYPDVN DFTLRFGVKD SNKNSVRVMK ASSDMRKNAQ ELLEPVLSER EMALNSNTSL E NDRNDDDD ...String: MSEYMDDVDR EFINCLFPSY LLQQPVAYDL WILYLQHRKL FHKLKNTNLI NADENPTGVG MGRTKLTALT RKEIWSKLMN LGVLGTISF EAVNDDYLIQ VYKYFYPDVN DFTLRFGVKD SNKNSVRVMK ASSDMRKNAQ ELLEPVLSER EMALNSNTSL E NDRNDDDD DDDDDDDDDD DDDDDDDESD LESLEGEVDT DTDDNNEGDG SDNHEEGGEE GSRGADADVS SAQQRAERVA DP WIYQRSR SAINIETESR NLWDTSDKNS GLQYYPPDQS PSSSFSSPRV SSGNDKNDNE ATNVLSNSGS KKKNSMIPDI YKI LGYFLP SRWQAQPNNS LQLSQDGITH LQPNPDYHSY MTYERSSASS ASTRNRLRTS FENSGKVDFA VTWANKSLPD NKLT IFYYE IKVLSVTSTE SAENSNIVIG YKLVENELME ATTKKSVSRS SVAGSSSSLG GSNNMSSNRV PSTSFTMEGT QRRDY IYEG GVSAMSLNVD GSINKCQKYG FDLNVFGYCG FDGLITNSTE QSKEYAKPFG RDDVIGCGIN FIDGSIFFTK NGIHLG NAF TDLNDLEFVP YVALRPGNSI KTNFGLNEDF VFDIIGYQDK WKSLAYEHIC RGRQMDVSIE EFDSDESEED ETENGPE EN KSTNVNEDLM DIDQEDGAAG NKDTKKLNDE KDNNLKFLLG EDNRFIDGKL VRPDVNNINN LSVDDGSLPN TLNVMIND Y LIHEGLVDVA KGFLKDLQKD AVNVNGQHSE SKDVIRHNER QIMKEERMVK IRQELRYLIN KGQISKCINY IDNEIPDLL KNNLELVFEL KLANYLVMIK KSSSKDDDEI ENLILKGQEL SNEFIYDTKI PQSLRDRFSG QLSNVSALLA YSNPLVEAPK EISGYLSDE YLQERLFQVS NNTILTFLHK DSECALENVI SNTRAMLSTL LEYNAFGSTN SSDPRYYKAI NFDEDVLNL UniProtKB: BJ4_G0038950.mRNA.1.CDS.1 |
-Macromolecule #4: Vacuolar import and degradation protein 24
Macromolecule | Name: Vacuolar import and degradation protein 24 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 41.291934 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MINNPKVDSV AEKPKAVTSK QSEQAASPEP TPAPPVSRNQ YPITFNLTST APFHLHDRHR YLQEQDLYKC ASRDSLSSLQ QLAHTPNGS TRKKYIVEDQ SPYSSENPVI VTSSYNHTVC TNYLRPRMQF TGYQISGYKR YQVTVNLKTV DLPKKDCTSL S PHLSGFLS ...String: MINNPKVDSV AEKPKAVTSK QSEQAASPEP TPAPPVSRNQ YPITFNLTST APFHLHDRHR YLQEQDLYKC ASRDSLSSLQ QLAHTPNGS TRKKYIVEDQ SPYSSENPVI VTSSYNHTVC TNYLRPRMQF TGYQISGYKR YQVTVNLKTV DLPKKDCTSL S PHLSGFLS IRGLTNQHPE ISTYFEAYAV NHKELGFLSS SWKDEPVLNE FKATDQTDLE HWINFPSFRQ LFLMSQKNGL NS TDDNGTT NAAKKLPPQQ LPTTPSADAG NISRIFSQEK QFDNYLNERF IFMKWKEKFL VPDALLMEGV DGASYDGFYY IVH DQVTGN IQGFYYHQDA EKFQQLELVP SLKNKVESSD CSFEFA UniProtKB: Vacuolar import and degradation protein 24 |
-Macromolecule #5: HLJ1_G0042170.mRNA.1.CDS.1
Macromolecule | Name: HLJ1_G0042170.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 81.564578 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MATGRIQFAV STPCNTKGKP SGYRLFEFKN DRLALVPSER GCTKVDVNAN IQAFCYLRPN GRDTSISPDA THILDSCDYM VLAKSNGFI EIISNYQYKI KNGLRLAPSY ILRCTPEDFE SNFFSDYMIA GLEYSQGLLY CCMCSGRIYV FVMNLPTDYI Q YKNMYNPM ...String: MATGRIQFAV STPCNTKGKP SGYRLFEFKN DRLALVPSER GCTKVDVNAN IQAFCYLRPN GRDTSISPDA THILDSCDYM VLAKSNGFI EIISNYQYKI KNGLRLAPSY ILRCTPEDFE SNFFSDYMIA GLEYSQGLLY CCMCSGRIYV FVMNLPTDYI Q YKNMYNPM FPDCFFKVHH DNNTTHSSEE EKLFEGSTRY TGRSCSKHIC YFLLPIEPSH LRSSPVVSSF CNMYQGLPIY RP SMYLHIE RGISTFHINP LDRFCFMTVS PRSPLFIRKI ILPLTYVTFL STFISLKNSI QGDTCGEILS WDNVAQQNGF GSL FSWISN KFTFDTDIIN STIWDDIVKY SGTGMLDSGI VWKQRQGHAK DDIYELFHTQ DMLGSSRRNS SFSTASSEPR PLSR RRRES FQALTRDAFR ERMDVPCSTK WELDSFIRGL RRNTFMVDFE IVEKISHRNG NDGVNEDDNT TDESDETMTS FLTDN YKKM DIVCIDHFVT LSAFRPRYYD EPIIKIDSLS NKNGSENGTN EEEWAESQMK VDGQVIDDET AQFKQALGNL CSFKKL FML DDSLCFILDT HGVLLINRFE IKNTKNLLRN SKDTIRIIPH DFGLINDTIV IINDIDVGTD NVCALTFHLV VTSMAGE IT VLKGEFFKNC RLGRIKLCDS LKLNRKDRFV DKLALIDYDG LNAQKRRLDY DEKDLYTFIV KKVKRD UniProtKB: YDL176W isoform 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 6.5 / Details: 25mM MES pH6.5 + 500mM NaCl + 1mM DTT |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 39 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.335 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |