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- EMDB-19039: Map of YPEL5-bound WDR26 dimer obtained by focused refinement of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19039
TitleMap of YPEL5-bound WDR26 dimer obtained by focused refinement of the WDR26-CTLH subcomplex
Map data
Sample
  • Complex: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WDR26 and YPEL5
KeywordsGID / CTLH / WDR26 / YPEL5 / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsChrustowicz J / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)UPSmeetMet, 101098161European Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: FEBS Lett / Year: 2024
Title: Skraban-Deardorff intellectual disability syndrome-associated mutations in WDR26 impair CTLH E3 complex assembly.
Authors: Annette Gross / Judith Müller / Jakub Chrustowicz / Alexander Strasser / Karthik V Gottemukkala / Dawafuti Sherpa / Brenda A Schulman / Peter J Murray / Arno F Alpi /
Abstract: Patients with Skraban-Deardorff syndrome (SKDEAS), a neurodevelopmental syndrome associated with a spectrum of developmental and intellectual delays and disabilities, harbor diverse mutations in ...Patients with Skraban-Deardorff syndrome (SKDEAS), a neurodevelopmental syndrome associated with a spectrum of developmental and intellectual delays and disabilities, harbor diverse mutations in WDR26, encoding a subunit of the multiprotein CTLH E3 ubiquitin ligase complex. Structural studies revealed that homodimers of WDR26 bridge two core-CTLH E3 complexes to generate giant, hollow oval-shaped supramolecular CTLH E3 assemblies. Additionally, WDR26 mediates CTLH E3 complex binding to subunit YPEL5 and functions as substrate receptor for the transcriptional repressor HBP1. Here, we mapped SKDEAS-associated mutations on a WDR26 structural model and tested their functionality in complementation studies using genetically engineered human cells lacking CTLH E3 supramolecular assemblies. Despite the diversity of mutations, 15 of 16 tested mutants impaired at least one CTLH E3 complex function contributing to complex assembly and interactions, thus providing first mechanistic insights into SKDEAS pathology.
History
DepositionDec 5, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19039.png

Downloads & links

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Map

FileDownload / File: emd_19039.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.21 Å/pix.
x 128 pix.
= 411.392 Å		3.21 Å/pix.
x 128 pix.
= 411.392 Å		3.21 Å/pix.
x 128 pix.
= 411.392 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.214 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.053
Minimum - Maximum-0.13033356 - 0.3286849
Average (Standard dev.)0.00027773587 (±0.006392154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 411.392 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19039_msk_1.map
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Half map: #1

Fileemd_19039_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_19039_half_map_2.map
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Sample components

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Entire : WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WD...

EntireName: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WDR26 and YPEL5
Components
  • Complex: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WDR26 and YPEL5

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Supramolecule #1: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WD...

SupramoleculeName: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WDR26 and YPEL5
type: complex / ID: 1 / Parent: 0
Details: Map obtained by focused refinement of the previously published map (EMD-12545) over the YPEL5-bound WDR26 dimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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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: 75.0 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:

12545

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26628
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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