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- EMDB-35492: The cryo-EM structure of human sphingomyelin synthase-related pro... -

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Entry
Database: EMDB / ID: EMD-35492
TitleThe cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
Map data
Sample
  • Complex: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
    • Protein or peptide: Sphingomyelin synthase-related protein 1
  • Ligand: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
Keywordssynthase / sphingomyelin / CPE / membrane protein / lipid metabolism
Function / homology
Function and homology information


ceramide phosphoethanolamine biosynthetic process / ceramide phosphoethanolamine synthase activity / sphingomyelin synthase activity / ceramide cholinephosphotransferase activity / regulation of ceramide biosynthetic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / sphingomyelin biosynthetic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / ceramide biosynthetic process ...ceramide phosphoethanolamine biosynthetic process / ceramide phosphoethanolamine synthase activity / sphingomyelin synthase activity / ceramide cholinephosphotransferase activity / regulation of ceramide biosynthetic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / sphingomyelin biosynthetic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / ceramide biosynthetic process / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol
Similarity search - Function
Sphingomyelin synthase-like / Sphingomyelin synthase-like domain / PAP2 superfamily C-terminal / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Sphingomyelin synthase-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsHu K / Zhang Q / Chen Y / Yao D / Zhou L / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
National Natural Science Foundation of China (NSFC)82272519 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis.
Authors: Kexin Hu / Qing Zhang / Yang Chen / Jintong Yang / Ying Xia / Bing Rao / Shaobai Li / Yafeng Shen / Mi Cao / Hongliang Lu / An Qin / Xian-Cheng Jiang / Deqiang Yao / Jie Zhao / Lu Zhou / Yu Cao /
Abstract: Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) ...Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) family, comprising SMS1, SMS2 and SMS-related (SMSr) members. Although SMS1 and SMS2 exhibit SMS activity, SMSr possesses ceramide phosphoethanolamine synthase activity. Here we determined the cryo-electron microscopic structures of human SMSr in complexes with ceramide, diacylglycerol/phosphoethanolamine and ceramide/phosphoethanolamine (CPE). The structures revealed a hexameric arrangement with a reaction chamber located between the transmembrane helices. Within this structure, a catalytic pentad E-H/D-H-D was identified, situated at the interface between the lipophilic and hydrophilic segments of the reaction chamber. Additionally, the study unveiled the two-step synthesis process catalyzed by SMSr, involving PE-PLC (phosphatidylethanolamine-phospholipase C) hydrolysis and the subsequent transfer of the phosphoethanolamine moiety to ceramide. This research provides insights into the catalytic mechanism of SMSr and expands our understanding of sphingolipid metabolism.
History
DepositionFeb 27, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35492.png

Downloads & links

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Map

FileDownload / File: emd_35492.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.3505754 - 5.52717
Average (Standard dev.)0.0031388868 (±0.086313605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 325.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35492_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35492_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : The cryo-EM structure of human sphingomyelin synthase-related pro...

EntireName: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
Components
  • Complex: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
    • Protein or peptide: Sphingomyelin synthase-related protein 1
  • Ligand: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE

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Supramolecule #1: The cryo-EM structure of human sphingomyelin synthase-related pro...

SupramoleculeName: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sphingomyelin synthase-related protein 1

MacromoleculeName: Sphingomyelin synthase-related protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: sphingomyelin synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.056529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RLDPEYWKTI LSCIYVFIVF GFTSFIMVIV HERVPDMQTY PPLPDIFLDS VPRIPWAFAM TEVCGMILCY IWLLVLLLHK HRSILLRRL CSLMGTVFLL RCFTMFVTSL SVPGQHLQCT GKIYGSVWEK LHRAFAIWSG FGMTLTGVHT CGDYMFSGHT V VLTMLNFF ...String:
RLDPEYWKTI LSCIYVFIVF GFTSFIMVIV HERVPDMQTY PPLPDIFLDS VPRIPWAFAM TEVCGMILCY IWLLVLLLHK HRSILLRRL CSLMGTVFLL RCFTMFVTSL SVPGQHLQCT GKIYGSVWEK LHRAFAIWSG FGMTLTGVHT CGDYMFSGHT V VLTMLNFF VTEYTPRSWN FLHTLSWVLN LFGIFFILAA HEHYSIDVFI AFYITTRLFL YYHTLANTRA YQQSRRARIW FP MFSFFEC NVNGTVPNEY CWPFSKP

UniProtKB: Sphingomyelin synthase-related protein 1

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Macromolecule #2: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE

MacromoleculeName: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
type: ligand / ID: 2 / Number of copies: 6 / Formula: 16C
Molecular weightTheoretical: 537.901 Da
Chemical component information

ChemComp-16C:
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 464274
FSC plot (resolution estimation)

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