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- EMDB-12564: Substrate receptor scaffolding module of human CTLH E3 ubiquitin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12564
TitleSubstrate receptor scaffolding module of human CTLH E3 ubiquitin ligase
Map data
SampleSRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
  • Ran-binding protein 9
  • Isoform 2 of Armadillo repeat-containing protein 8
  • (Glucose-induced degradation protein ...) x 2
Function / homology
Function and homology information


GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / ubiquitin ligase complex / cytoskeleton organization / MET activates RAS signaling / negative regulation of ERK1 and ERK2 cascade / small GTPase binding ...GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / ubiquitin ligase complex / cytoskeleton organization / MET activates RAS signaling / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / specific granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / axon guidance / cell junction / protein-containing complex assembly / Wnt signaling pathway / tertiary granule lumen / RAF/MAP kinase cascade / nuclear body / cell surface receptor signaling pathway / MAPK cascade / intracellular membrane-bounded organelle / Neutrophil degranulation / neutrophil degranulation / positive regulation of cell population proliferation / enzyme binding / protein homodimerization activity / extracellular region / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / CT11-RanBPM / CRA domain / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import and degradation protein / Vacuolar import/degradation protein Vid24 / LisH / C-terminal to LisH motif. ...Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / CT11-RanBPM / CRA domain / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import and degradation protein / Vacuolar import/degradation protein Vid24 / 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 / B30.2/SPRY domain superfamily / SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain / Armadillo/beta-catenin-like repeats / Domain in SPla and the RYanodine Receptor. / Armadillo / SPRY domain / Armadillo-like helical / Armadillo-type fold / Concanavalin A-like lectin/glucanase domain superfamily
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nsc
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12564.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.2 Å
0.85 Å/pix.
x 352 pix.
= 299.2 Å
0.85 Å/pix.
x 352 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.0245 / Movie #1: 0.0245
Minimum - Maximum-0.07453973 - 0.12510686
Average (Standard dev.)8.618144e-05 (±0.0022115025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z299.200299.200299.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0750.1250.000

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Supplemental data

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Segmentation: #1

Fileemd_12564_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_12564_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_12564_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_12564_half_map_2.map
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Sample components

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Entire SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 a...

EntireName: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
Details: Generated by focused refinement of CTLH SR4 map / Number of components: 5

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Component #1: protein, SRS module of human CTLH complex comprising RANBP9, TWA1...

ProteinName: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
Details: Generated by focused refinement of CTLH SR4 map / Recombinant expression: No
MassTheoretical: 210 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Ran-binding protein 9

ProteinName: Ran-binding protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 77.927062 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Isoform 2 of Armadillo repeat-containing protein 8

ProteinName: Isoform 2 of Armadillo repeat-containing protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.082297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, Glucose-induced degradation protein 8 homolog

ProteinName: Glucose-induced degradation protein 8 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.796715 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, Glucose-induced degradation protein 4 homolog

ProteinName: Glucose-induced degradation protein 4 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.559906 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 78264
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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