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- EMDB-16242: Cryo-EM structure of RANBP10-CTLH SR4 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-16242
TitleCryo-EM structure of RANBP10-CTLH SR4 complex
Map data
Sample
  • Complex: RANBP10-CTLH SR4 complex
KeywordsCTLH / E3 ubiquitin ligase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.64 Å
AuthorsSherpa D / Chrustowicz J
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Elife / Year: 2022
Title: Modular UBE2H-CTLH E2-E3 complexes regulate erythroid maturation.
Authors: Dawafuti Sherpa / Judith Mueller / Özge Karayel / Peng Xu / Yu Yao / Jakub Chrustowicz / Karthik V Gottemukkala / Christine Baumann / Annette Gross / Oliver Czarnecki / Wei Zhang / Jun Gu / ...Authors: Dawafuti Sherpa / Judith Mueller / Özge Karayel / Peng Xu / Yu Yao / Jakub Chrustowicz / Karthik V Gottemukkala / Christine Baumann / Annette Gross / Oliver Czarnecki / Wei Zhang / Jun Gu / Johan Nilvebrant / Sachdev S Sidhu / Peter J Murray / Matthias Mann / Mitchell J Weiss / Brenda A Schulman / Arno F Alpi /
Abstract: The development of haematopoietic stem cells into mature erythrocytes - erythropoiesis - is a controlled process characterized by cellular reorganization and drastic reshaping of the proteome ...The development of haematopoietic stem cells into mature erythrocytes - erythropoiesis - is a controlled process characterized by cellular reorganization and drastic reshaping of the proteome landscape. Failure of ordered erythropoiesis is associated with anaemias and haematological malignancies. Although the ubiquitin system is a known crucial post-translational regulator in erythropoiesis, how the erythrocyte is reshaped by the ubiquitin system is poorly understood. By measuring the proteomic landscape of in vitro human erythropoiesis models, we found dynamic differential expression of subunits of the CTLH E3 ubiquitin ligase complex that formed maturation stage-dependent assemblies of topologically homologous RANBP9- and RANBP10-CTLH complexes. Moreover, protein abundance of CTLH's cognate E2 ubiquitin conjugating enzyme UBE2H increased during terminal differentiation, and UBE2H expression depended on catalytically active CTLH E3 complexes. CRISPR-Cas9-mediated inactivation of CTLH E3 assemblies or UBE2H in erythroid progenitors revealed defects, including spontaneous and accelerated erythroid maturation as well as inefficient enucleation. Thus, we propose that dynamic maturation stage-specific changes of UBE2H-CTLH E2-E3 modules control the orderly progression of human erythropoiesis.
History
DepositionNov 30, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16242.png

Downloads & links

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Map

FileDownload / File: emd_16242.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 176 pix.
= 351.472 Å		2 Å/pix.
x 176 pix.
= 351.472 Å		2 Å/pix.
x 176 pix.
= 351.472 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.997 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.0658193 - 0.27938652
Average (Standard dev.)0.0007378375 (±0.0095855845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 351.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16242_msk_1.map
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Additional map: #1

Fileemd_16242_additional_1.map
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Half map: #2

Fileemd_16242_half_map_1.map
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Half map: #1

Fileemd_16242_half_map_2.map
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Sample components

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Entire : RANBP10-CTLH SR4 complex

EntireName: RANBP10-CTLH SR4 complex
Components
  • Complex: RANBP10-CTLH SR4 complex

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Supramolecule #1: RANBP10-CTLH SR4 complex

SupramoleculeName: RANBP10-CTLH SR4 complex / type: complex / ID: 1 / Parent: 0 / Details: RANBP10, TWA1, ARMC8, RMND5A, MAEA, GID4
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.8 mg/mL
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: 69.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12537

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13430
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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