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- EMDB-17717: SRS and Cat modules of yeast Chelator-GIDSR4 bound to multiphosph... -

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Basic information

Entry
Database: EMDB / ID: EMD-17717
TitleSRS and Cat modules of yeast Chelator-GIDSR4 bound to multiphosphorylated Ubc8~ubiquitin
Map data
Sample
  • Complex: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
KeywordsE3 ubiquitin ligase / E2 ubiquitin-conjugating enzyme / phosphorylation / GID / LIGASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChrustowicz J / Sherpa D / Schulman BA
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)H2020 789016-NEDD8ActivateEuropean Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Mol Cell / Year: 2024
Title: Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies.
Authors: Jakub Chrustowicz / Dawafuti Sherpa / Jerry Li / Christine R Langlois / Eleftheria C Papadopoulou / D Tung Vu / Laura A Hehl / Özge Karayel / Viola Beier / Susanne von Gronau / Judith ...Authors: Jakub Chrustowicz / Dawafuti Sherpa / Jerry Li / Christine R Langlois / Eleftheria C Papadopoulou / D Tung Vu / Laura A Hehl / Özge Karayel / Viola Beier / Susanne von Gronau / Judith Müller / J Rajan Prabu / Matthias Mann / Gary Kleiger / Arno F Alpi / Brenda A Schulman /
Abstract: Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ...Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.
History
DepositionJun 23, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17717.png

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Map

FileDownload / File: emd_17717.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 272 pix.
= 388.144 Å		1.43 Å/pix.
x 272 pix.
= 388.144 Å		1.43 Å/pix.
x 272 pix.
= 388.144 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.427 Å
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Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.023519378 - 0.05371702
Average (Standard dev.)0.000073939285 (±0.001765116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 388.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17717_msk_1.map
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Half map: #2

Fileemd_17717_half_map_1.map
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Half map: #1

Fileemd_17717_half_map_2.map
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Sample components

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Entire : Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 subst...

EntireName: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
Components
  • Complex: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin

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Supramolecule #1: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 subst...

SupramoleculeName: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Focused refinement over the substrate receptor-scaffolding (SRS: Gid1, Gid8, Gid5, Gid4) and catalytic (Cat: Gid2, Gid9) modules and Ubc8~ubiquitin
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.7 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
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: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60079
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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