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- PDB-8w9y: The cryo-EM structure of human sphingomyelin synthase-related protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 8w9y | |||||||||
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Title | The cryo-EM structure of human sphingomyelin synthase-related protein | |||||||||
![]() | Sphingomyelin synthase-related protein 1 | |||||||||
![]() | MEMBRANE PROTEIN / synthase / sphingomyelin / CPE / lipid metabolism | |||||||||
Function / homology | ![]() 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 / endoplasmic reticulum 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 / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Hu, K. / Zhang, Q. / Chen, Y. / Yao, D. / Zhou, L. / Cao, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284.1 KB | Display | ![]() |
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PDB format | ![]() | 236.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391.2 KB | Display | ![]() |
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Full document | ![]() | 412.6 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37385MC ![]() 8ijqC ![]() 8ijrC ![]() 8w9wC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 31056.529 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The cryo-EM structure of human sphingomyelin synthase-related protein Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 352573 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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