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- PDB-7nsc: Substrate receptor scaffolding module of human CTLH E3 ubiquitin ... -

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Basic information

Entry
Database: PDB / ID: 7nsc
TitleSubstrate receptor scaffolding module of human CTLH E3 ubiquitin ligase
Components
  • Glucose-induced degradation protein 4 homolog
  • Glucose-induced degradation protein 8 homolog
  • Isoform 2 of Armadillo repeat-containing protein 8
  • Ran-binding protein 9
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM
Function / homology
Function and homology information


GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / Regulation of pyruvate metabolism / negative regulation of ERK1 and ERK2 cascade ...GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / Regulation of pyruvate metabolism / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / small GTPase binding / specific granule lumen / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / cell junction / tertiary granule lumen / RAF/MAP kinase cascade / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / Neutrophil degranulation / enzyme binding / protein homodimerization activity / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / LisH ...Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / 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 / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Armadillo repeat-containing protein 8 / Glucose-induced degradation protein 4 homolog / Ran-binding protein 9 / Glucose-induced degradation protein 8 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChrustowicz, J. / Sherpa, D. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 2items
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, C.R. / Hehl, L.A. / Gottemukkala, K.V. / Hansen, F.M. / Karayel, O. / Prabu, J.R. / Mann, M. / Alpi, A.F. / Schulman, B.A.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.3Jun 9, 2021Group: Derived calculations / Category: struct_conf
Revision 1.4Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.5Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_admin
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Ran-binding protein 9
E: Isoform 2 of Armadillo repeat-containing protein 8
H: Glucose-induced degradation protein 8 homolog
D: Glucose-induced degradation protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)216,3664
Polymers216,3664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10880 Å2
ΔGint-59 kcal/mol
Surface area52470 Å2
MethodPISA

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Components

#1: Protein Ran-binding protein 9 / RanBP9 / BPM-L / BPM90 / Ran-binding protein M / RanBPM / RanBP7


Mass: 77927.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP9, RANBPM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96S59
#2: Protein Isoform 2 of Armadillo repeat-containing protein 8


Mass: 74082.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARMC8, S863-2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IUR7
#3: Protein Glucose-induced degradation protein 8 homolog / Two hybrid-associated protein 1 with RanBPM / Twa1


Mass: 30796.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID8, C20orf11, TWA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NWU2
#4: Protein Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 33559.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
Type: COMPLEX / Details: Generated by focused refinement of CTLH SR4 map / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78264 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049518
ELECTRON MICROSCOPYf_angle_d0.67612933
ELECTRON MICROSCOPYf_dihedral_angle_d17.2181309
ELECTRON MICROSCOPYf_chiral_restr0.0421506
ELECTRON MICROSCOPYf_plane_restr0.0041648

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