+
Open data
-
Basic information
Entry | Database: PDB / ID: 8c81 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex | |||||||||
![]() |
| |||||||||
![]() | TRANSFERASE / Serine-Palmitoyl-Transferase / SPT / Orm-Protein | |||||||||
Function / homology | ![]() Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / negative regulation of sphingolipid biosynthetic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane ...Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / negative regulation of sphingolipid biosynthetic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / serine palmitoyltransferase complex / : / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / autophagosome-lysosome fusion / cortical endoplasmic reticulum / sphingosine biosynthetic process / sphingolipid biosynthetic process / ceramide biosynthetic process / phosphatidylinositol dephosphorylation / Golgi medial cisterna / response to unfolded protein / enzyme activator activity / Neutrophil degranulation / pyridoxal phosphate binding / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Schaefer, J. / Koerner, C. / Parey, K. / Januliene, D. / Moeller, A. / Froehlich, F. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of the ceramide-bound SPOTS complex. Authors: Jan-Hannes Schäfer / Carolin Körner / Bianca M Esch / Sergej Limar / Kristian Parey / Stefan Walter / Dovile Januliene / Arne Moeller / Florian Fröhlich / ![]() Abstract: Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. ...Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 361.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 286.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 16468MC ![]() 8c80C ![]() 8c82C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 3 molecules ADE
#1: Protein | Mass: 25221.674 Da / Num. of mol.: 1 / Mutation: S51A, S52A, S53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ORM1, YGR038W / Production host: ![]() ![]() |
---|---|
#4: Protein | Mass: 9590.233 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TSC3, YBR058C-A / Production host: ![]() ![]() |
#5: Protein | Mass: 71214.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SAC1, RSD1, YKL212W / Production host: ![]() ![]() References: UniProt: P32368, phosphatidylinositol-3-phosphatase |
-Serine palmitoyltransferase ... , 2 types, 2 molecules BC
#2: Protein | Mass: 64985.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LCB1, END8, TSC2, YMR296C / Production host: ![]() ![]() |
---|---|
#3: Protein | Mass: 63189.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LCB2, SCS1, TSC1, YDR062W, D4246, YD9609.16 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 6 molecules ![](data/chem/img/ERG.gif)
![](data/chem/img/Z8A.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/Z8A.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PLP.gif)
#6: Chemical | #7: Chemical | ChemComp-Z8A / | #8: Chemical | ChemComp-Q7G / | #9: Chemical | ChemComp-PLP / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1 Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.23 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6.8 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-
Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 13604 |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 10 eV |
-
Processing
Software | Name: UCSF ChimeraX / Version: 1.6/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53236 / Symmetry type: POINT | ||||||||||
Atomic model building | B value: 63 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||
Refinement | Highest resolution: 3.3 Å |