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Yorodumi- EMDB-12547: Structure of supramolecular assembly and substrate receptor scaff... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12547 | |||||||||
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Title | Structure of supramolecular assembly and substrate receptor scaffolding modules of human CTLH-MKLN1 complex | |||||||||
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Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.1 Å | |||||||||
Authors | Chrustowicz J / Sherpa D / Schulman BA | |||||||||
Funding support | Germany, 2 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12547.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-12547-v30.xml emd-12547.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12547_fsc.xml | 4.4 KB | Display | FSC data file |
Images | emd_12547.png | 112.4 KB | ||
Masks | emd_12547_msk_1.map | 6.6 MB | Mask map | |
Others | emd_12547_additional_1.map.gz emd_12547_half_map_1.map.gz emd_12547_half_map_2.map.gz | 5.9 MB 5 MB 4.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12547 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12547.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 3.1165 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12547_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_12547_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_12547_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12547_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CTLH-MKLN1 subcomplex comprising RANBP9-TWA1-ARMC8-hGid4-MKLN1
Entire | Name: CTLH-MKLN1 subcomplex comprising RANBP9-TWA1-ARMC8-hGid4-MKLN1 |
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Components |
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-Supramolecule #1: CTLH-MKLN1 subcomplex comprising RANBP9-TWA1-ARMC8-hGid4-MKLN1
Supramolecule | Name: CTLH-MKLN1 subcomplex comprising RANBP9-TWA1-ARMC8-hGid4-MKLN1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 550 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 71.7 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |