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Yorodumi- EMDB-19039: Map of YPEL5-bound WDR26 dimer obtained by focused refinement of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19039 | |||||||||
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Title | Map of YPEL5-bound WDR26 dimer obtained by focused refinement of the WDR26-CTLH subcomplex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | GID / CTLH / WDR26 / YPEL5 / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM / LIGASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Chrustowicz J / Schulman BA | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19039.map.gz | 671 KB | EMDB map data format | |
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Header (meta data) | emd-19039-v30.xml emd-19039.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19039_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_19039.png | 157.3 KB | ||
Masks | emd_19039_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-19039.cif.gz | 4.1 KB | ||
Others | emd_19039_half_map_1.map.gz emd_19039_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19039 | HTTPS FTP |
-Related structure data
Related structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19039.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.214 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19039_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19039_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_19039_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WD...
Entire | Name: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WDR26 and YPEL5 |
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Components |
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-Supramolecule #1: WDR26-CTLH E3 subcomplex comprising RANBP9, TWA1, ARMC8, GID4, WD...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 300 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |