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- EMDB-12563: Supramolecular assembly module of yeast Chelator-GID SR4 E3 ubiqu... -

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Basic information

Entry
Database: EMDB / ID: EMD-12563
TitleSupramolecular assembly module of yeast Chelator-GID SR4 E3 ubiquitin ligase
Map data
Sample
  • Complex: Supramolecular assembly module of yeast Chelator-GID SR4 comprising Gid1, Gid8 and a homodimer of Gid7
    • Protein or peptide: Vacuolar import and degradation protein 30
    • Protein or peptide: Glucose-induced degradation protein 7
    • Protein or peptide: Glucose-induced degradation protein 8
KeywordsGID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM / LIGASE
Function / homology
Function and homology information


GID complex / Regulation of pyruvate metabolism / traversing start control point of mitotic cell cycle / regulation of nitrogen utilization / negative regulation of gluconeogenesis / cytoskeleton organization / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / : / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / : / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Glucose-induced degradation protein 7 / Glucose-induced degradation protein 8 / Vacuolar import and degradation protein 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChrustowicz J / Sherpa D / Prabu JR / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Citation
Journal: Mol Cell / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme.
Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / ...Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / Matthias Mann / Arno F Alpi / Brenda A Schulman /
Abstract: How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of ...How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GID, which resembles an organometallic supramolecular chelate. The Chelator-GID assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
#1: Journal: Biorxiv / 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 / Prabu JR / Mann M / Alpi AF / Schulman BA
History
DepositionMar 5, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nsb
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12563.png

Downloads & links

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Map

FileDownload / File: emd_12563.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 288 pix.
= 455.04 Å		1.58 Å/pix.
x 288 pix.
= 455.04 Å		1.58 Å/pix.
x 288 pix.
= 455.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.13553758 - 0.23278113
Average (Standard dev.)0.000067103785 (±0.003022662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 455.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z455.040455.040455.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1360.2330.000

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Supplemental data

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Mask #1

Fileemd_12563_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_12563_additional_1.map
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Half map: #2

Fileemd_12563_half_map_1.map
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Half map: #1

Fileemd_12563_half_map_2.map
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Sample components

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Entire : Supramolecular assembly module of yeast Chelator-GID SR4 comprisi...

EntireName: Supramolecular assembly module of yeast Chelator-GID SR4 comprising Gid1, Gid8 and a homodimer of Gid7
Components
  • Complex: Supramolecular assembly module of yeast Chelator-GID SR4 comprising Gid1, Gid8 and a homodimer of Gid7
    • Protein or peptide: Vacuolar import and degradation protein 30
    • Protein or peptide: Glucose-induced degradation protein 7
    • Protein or peptide: Glucose-induced degradation protein 8

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Supramolecule #1: Supramolecular assembly module of yeast Chelator-GID SR4 comprisi...

SupramoleculeName: Supramolecular assembly module of yeast Chelator-GID SR4 comprising Gid1, Gid8 and a homodimer of Gid7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Generated by focused refinement of Chelator-GID SR4 + Fbp1 map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: Vacuolar import and degradation protein 30

MacromoleculeName: Vacuolar import and degradation protein 30 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 108.28768 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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: Vacuolar import and degradation protein 30

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Macromolecule #2: Glucose-induced degradation protein 7

MacromoleculeName: Glucose-induced degradation protein 7 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 84.607297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHTNKIAYV LNNDTEETAS PSSVGCFDKK QLTKLLIHTL KELGYDSAAN QLLLESGGYQ NESNHIQTFF KLIKTGQFHL INWQIVCSL PLAHSSPLRS EWLQRLLIPT PTPATTSLFD HMLLQLQYLQ QLMSSVNSST CSDAEIATLR NYVEIMILVN R QIFLEFFH ...String:
MSHTNKIAYV LNNDTEETAS PSSVGCFDKK QLTKLLIHTL KELGYDSAAN QLLLESGGYQ NESNHIQTFF KLIKTGQFHL INWQIVCSL PLAHSSPLRS EWLQRLLIPT PTPATTSLFD HMLLQLQYLQ QLMSSVNSST CSDAEIATLR NYVEIMILVN R QIFLEFFH PVTNSASHKG PHTALPVLYL RKILKNFIEI WDSLLVSNDQ FLNEENIFNP ETTLRELSTY LTNPKLTAQL NL ERDHLID AISKYIDPNE LVPKGRLLHL LKQAIKYQQS QDIFNIIDPD DDASFSSPPH RINLLQDNFS HDLTVTFQEW KTI QDTTDE IWFLTFSPNG KYLASATSES SRGYFITVYD VEQDFKIYKT CVSLSQSVLY LMFSPDSRYL VACPFSEDVT IYDM NATSL PDASATDSFL LYPSTRLSPM DSFKLDTTTY PDDTESSASS SSRPANANSN QSRVWCCDAF HTAERAGWMV VGSPD REAI VHSLTTKESL FSLKGRTCIA LGHDENISGR KSIDPAKVLY KPTSSNGNWQ YVEDDETFPR VHDVKISYDD KYVLLM THQ GVIDVYDFSG FPSKEELSKQ TVDPKNFLIP RIARLDVGKN MTCISLPLNT THQGFHRQQI SESQHLVLVS LQDNELQ MW DYKENILIQK YFGQKQQHFI IRSCFAYGNK LVMSGSEDGK IYIWDRIRGN LVSVLSGHST VMSNSTKPMG KNCNVVAS N PADKEMFASG GDDGKIKIWK ISRN

UniProtKB: Glucose-induced degradation protein 7

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Macromolecule #3: Glucose-induced degradation protein 8

MacromoleculeName: Glucose-induced degradation protein 8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.803309 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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 SDENLYFQSG WSHPQFEKGG GSGGG SGGS AWSHPQFEK

UniProtKB: Glucose-induced degradation protein 8

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12557

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48629
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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