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- EMDB-12542: Structure of human CTLH-WDR26 supramolecular assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-12542
TitleStructure of human CTLH-WDR26 supramolecular assembly
Map data
Sample
  • Complex: CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.2 Å
AuthorsChrustowicz J / Sherpa D / 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 3, 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: 0.0805
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0805
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12542.png

Downloads & links

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Map

FileDownload / File: emd_12542.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 88 pix.
= 383.425 Å		4.36 Å/pix.
x 88 pix.
= 383.425 Å		4.36 Å/pix.
x 88 pix.
= 383.425 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0805 / Movie #1: 0.0805
Minimum - Maximum-0.050110474 - 0.2561897
Average (Standard dev.)0.0049955365 (±0.02955797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions888888
Spacing888888
CellA=B=C: 383.4248 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.35710227272734.35710227272734.3571022727273
M x/y/z888888
origin x/y/z0.0000.0000.000
length x/y/z383.425383.425383.425
α/β/γ90.00090.00090.000
start NX/NY/NZ696888
NX/NY/NZ828048
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS888888
D min/max/mean-0.0500.2560.005

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Supplemental data

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Mask #1

Fileemd_12542_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_12542_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12542_half_map_2.map
Projections & Slices
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Sample components

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Entire : CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26

EntireName: CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26
Components
  • Complex: CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26

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Supramolecule #1: CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26

SupramoleculeName: CTLH-WDR26 complex comprising RANBP9-TWA1-ARMC8-RMND5A-MAEA-WDR26
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 1.3 MDa

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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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 75.36 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 19.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2802
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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