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- EMDB-35493: The cryo-EM structure of human sphingomyelin synthase-related pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-35493
TitleThe cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine
Map data
Sample
  • Complex: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine
    • Protein or peptide: Sphingomyelin synthase-related protein 1
  • Ligand: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
  • Ligand: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER
Keywordssynthase / sphingomyelin / CPE / membrane protein / lipid metabolism
Function / homology
Function and homology information


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 de novo biosynthesis / ceramide biosynthetic process / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum ...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 de novo biosynthesis / ceramide biosynthetic process / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / plasma membrane / cytosol
Similarity search - Function
Sphingomyelin synthase-like domain / Sphingomyelin synthase-like / 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: 3.29 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 28, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35493.png

Downloads & links

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Map

FileDownload / File: emd_35493.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 296 pix.
= 325.6 Å		1.1 Å/pix.
x 296 pix.
= 325.6 Å		1.1 Å/pix.
x 296 pix.
= 325.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.478566 - 7.24129
Average (Standard dev.)0.0012466299 (±0.106759824)
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_35493_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35493_half_map_2.map
Projections & Slices
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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 diacylglycerol/phosphoethanolamine
Components
  • Complex: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine
    • Protein or peptide: Sphingomyelin synthase-related protein 1
  • Ligand: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
  • Ligand: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER

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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 diacylglycerol/phosphoethanolamine
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: 48.373473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGPNQLCIR RWTTKHVAVW LKDEGFFEYV DILCNKHRLD GITLLTLTEY DLRSPPLEIK VLGDIKRLML SVRKLQKIHI DVLEEMGYN SDSPMGSMTP FISALQSTDW LCNGELSHDC DGPITDLNSD QYQYMNGKNK HSVRRLDPEY WKTILSCIYV F IVFGFTSF ...String:
MAGPNQLCIR RWTTKHVAVW LKDEGFFEYV DILCNKHRLD GITLLTLTEY DLRSPPLEIK VLGDIKRLML SVRKLQKIHI DVLEEMGYN SDSPMGSMTP FISALQSTDW LCNGELSHDC DGPITDLNSD QYQYMNGKNK HSVRRLDPEY WKTILSCIYV F IVFGFTSF IMVIVHERVP DMQTYPPLPD IFLDSVPRIP WAFAMTEVCG MILCYIWLLV LLLHKHRSIL LRRLCSLMGT VF LLRCFTM FVTSLSVPGQ HLQCTGKIYG SVWEKLHRAF AIWSGFGMTL TGVHTCGDYM FSGHTVVLTM LNFFVTEYTP RSW NFLHTL SWVLNLFGIF FILAAHEHYS IDVFIAFYIT TRLFLYYHTL ANTRAYQQSR RARIWFPMFS FFECNVNGTV PNEY CWPFS KPAIMKRLIG

UniProtKB: Sphingomyelin synthase-related protein 1

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Macromolecule #2: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
type: ligand / ID: 2 / Number of copies: 6 / Formula: Z0P
Molecular weightTheoretical: 594.949 Da
Chemical component information

ChemComp-Z0P:
(2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate

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Macromolecule #3: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER

MacromoleculeName: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: OPE
Molecular weightTheoretical: 141.063 Da
Chemical component information

ChemComp-OPE:
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER

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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 761985
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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