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- EMDB-18533: Cryo-EM structure of the yeast SPT-Orm2-Dimer complex, local refi... -

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Basic information

Entry
Database: EMDB / ID: EMD-18533
TitleCryo-EM structure of the yeast SPT-Orm2-Dimer complex, local refinement of a monomer
Map dataMap-Full
Sample
  • Complex: Complex of Lcb1, Lcb2, Orm2 and Tsc3
KeywordsSerine-Palmitoyl-Transferase / TRANSFERASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSchaefer J / Koerner C / Parey K / Januliene D / Moeller A / Froehlich F
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557 Germany
CitationJournal: Cell Rep / Year: 2024
Title: The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins.
Authors: Carolin Körner / Jan-Hannes Schäfer / Bianca M Esch / Kristian Parey / Stefan Walter / David Teis / Dovile Januliene / Oliver Schmidt / Arne Moeller / Florian Fröhlich /
Abstract: Sphingolipid levels are crucial determinants of neurodegenerative disorders and therefore require tight regulation. The Orm protein family and ceramides inhibit the rate-limiting step of sphingolipid ...Sphingolipid levels are crucial determinants of neurodegenerative disorders and therefore require tight regulation. The Orm protein family and ceramides inhibit the rate-limiting step of sphingolipid biosynthesis-the condensation of L-serine and palmitoyl-coenzyme A (CoA). The yeast isoforms Orm1 and Orm2 form a complex with the serine palmitoyltransferase (SPT). While Orm1 and Orm2 have highly similar sequences, they are differentially regulated, though the mechanistic details remain elusive. Here, we determine the cryoelectron microscopy structure of the SPT complex containing Orm2. Complementary in vitro activity assays and genetic experiments with targeted lipidomics demonstrate a lower activity of the SPT-Orm2 complex than the SPT-Orm1 complex. Our results suggest a higher inhibitory potential of Orm2, despite the similar structures of the Orm1- and Orm2-containing complexes. The high conservation of SPT from yeast to man implies different regulatory capacities for the three human ORMDL isoforms, which might be key for understanding their role in sphingolipid-mediated neurodegenerative disorders.
History
DepositionSep 28, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18533.png

Downloads & links

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Map

FileDownload / File: emd_18533.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap-Full
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 384 pix.
= 354.816 Å		0.92 Å/pix.
x 384 pix.
= 354.816 Å		0.92 Å/pix.
x 384 pix.
= 354.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.89807767 - 1.490928
Average (Standard dev.)0.00032286474 (±0.039054498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 354.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18533_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half-A

Fileemd_18533_half_map_1.map
AnnotationHalf-A
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B

Fileemd_18533_half_map_2.map
AnnotationHalf-B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Lcb1, Lcb2, Orm2 and Tsc3

EntireName: Complex of Lcb1, Lcb2, Orm2 and Tsc3
Components
  • Complex: Complex of Lcb1, Lcb2, Orm2 and Tsc3

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Supramolecule #1: Complex of Lcb1, Lcb2, Orm2 and Tsc3

SupramoleculeName: Complex of Lcb1, Lcb2, Orm2 and Tsc3 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 160 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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148610
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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