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Yorodumi- EMDB-35493: The cryo-EM structure of human sphingomyelin synthase-related pro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35493 | |||||||||
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Title | The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine | |||||||||
Map data | ||||||||||
Sample |
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Keywords | synthase / 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 de novo biosynthesis / ceramide biosynthetic process / Golgi membrane ...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 de novo biosynthesis / ceramide biosynthetic process / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Hu K / Zhang Q / Chen Y / Yao D / Zhou L / Cao Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35493.map.gz | 93.2 MB | EMDB map data format | |
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Header (meta data) | emd-35493-v30.xml emd-35493.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35493_fsc.xml | 9.7 KB | Display | FSC data file |
Images | emd_35493.png | 69.9 KB | ||
Filedesc metadata | emd-35493.cif.gz | 5.6 KB | ||
Others | emd_35493_half_map_1.map.gz emd_35493_half_map_2.map.gz | 91.5 MB 91.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35493 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35493 | HTTPS FTP |
-Validation report
Summary document | emd_35493_validation.pdf.gz | 748 KB | Display | EMDB validaton report |
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Full document | emd_35493_full_validation.pdf.gz | 747.6 KB | Display | |
Data in XML | emd_35493_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_35493_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35493 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35493 | HTTPS FTP |
-Related structure data
Related structure data | 8ijrMC 8ijqC 8w9wC 8w9yC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35493.map.gz / Format: CCP4 / Size: 98.9 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35493_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35493_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The cryo-EM structure of human sphingomyelin synthase-related pro...
Entire | Name: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine |
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Components |
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-Supramolecule #1: The cryo-EM structure of human sphingomyelin synthase-related pro...
Supramolecule | Name: The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Sphingomyelin synthase-related protein 1
Macromolecule | Name: Sphingomyelin synthase-related protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: sphingomyelin synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.373473 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
Macromolecule | Name: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate type: ligand / ID: 2 / Number of copies: 6 / Formula: Z0P |
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Molecular weight | Theoretical: 594.949 Da |
Chemical component information | ChemComp-Z0P: |
-Macromolecule #3: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER
Macromolecule | Name: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: OPE |
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Molecular weight | Theoretical: 141.063 Da |
Chemical component information | ChemComp-OPE: |
-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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |