+Open data
-Basic information
Entry | Database: PDB / ID: 7yiu | ||||||
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Title | Cryo-EM structure of the C6-ceramide-bound SPT-ORMDL3 complex | ||||||
Components |
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Keywords | TRANSFERASE/inhibitor / ceramide / TRANSFERASE-inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of ceramide biosynthetic process / sphinganine biosynthetic process / regulation of fat cell apoptotic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / : / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process ...negative regulation of ceramide biosynthetic process / sphinganine biosynthetic process / regulation of fat cell apoptotic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / : / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / regulation of smooth muscle contraction / sphingosine biosynthetic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingolipid metabolic process / ceramide biosynthetic process / negative regulation of B cell apoptotic process / motor behavior / positive regulation of lipophagy / adipose tissue development / positive regulation of autophagy / specific granule membrane / myelination / secretory granule membrane / protein localization / positive regulation of protein localization to nucleus / pyridoxal phosphate binding / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Xie, T. / Liu, P. / Gong, X. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Authors: Tian Xie / Peng Liu / Xinyue Wu / Feitong Dong / Zike Zhang / Jian Yue / Usha Mahawar / Faheem Farooq / Hisham Vohra / Qi Fang / Wenchen Liu / Binks W Wattenberg / Xin Gong / Abstract: The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This ...The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yiu.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yiu.ent.gz | 172.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yiu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yiu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yiu_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 7yiu_validation.cif.gz | 65.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/7yiu ftp://data.pdbj.org/pub/pdb/validation_reports/yi/7yiu | HTTPS FTP |
-Related structure data
Related structure data | 33864MC 7yiyC 7yj1C 7yj2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Serine palmitoyltransferase ... , 4 types, 4 molecules BECA
#1: Protein | Mass: 63004.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTLC2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15270, serine C-palmitoyltransferase |
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#2: Protein/peptide | Mass: 5898.994 Da / Num. of mol.: 1 / Fragment: UNP residues 1-50 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTLC1, LCB1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15269, serine C-palmitoyltransferase |
#4: Protein | Mass: 10742.409 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTSSA, C14orf147, SSSPTA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q969W0 |
#5: Protein | Mass: 46925.828 Da / Num. of mol.: 1 / Fragment: UNP residues 51-473 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTLC1, LCB1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15269, serine C-palmitoyltransferase |
-Protein , 1 types, 1 molecules D
#3: Protein | Mass: 17512.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORMDL3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N138 |
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-Non-polymers , 3 types, 4 molecules
#6: Chemical | ChemComp-PLP / |
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#7: Chemical | ChemComp-6CM / |
#8: Chemical |
-Details
Has ligand of interest | Y |
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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 |
-Sample preparation
Component | Name: SPT-ORMDL3 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) / Cell: HEK293 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337730 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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