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- PDB-7k0q: Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/OR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k0q | ||||||
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Title | Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, myriocin-bound | ||||||
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![]() | MEMBRANE PROTEIN / Sphingolipid | ||||||
Function / homology | ![]() sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / serine palmitoyltransferase complex / sphingomyelin biosynthetic process / : / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process ...sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / serine palmitoyltransferase complex / sphingomyelin biosynthetic process / : / 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 / positive regulation of protein localization to nucleus / protein localization / pyridoxal phosphate binding / endoplasmic reticulum membrane / Neutrophil degranulation / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Wang, Y. / Niu, Y. / Zhang, Z. / Zhao, H. / Myasnikov, A. / Kalathur, R. / Lee, C.H. | ||||||
![]() | ![]() Title: Structural insights into the regulation of human serine palmitoyltransferase complexes. Authors: Yingdi Wang / Yiming Niu / Zhe Zhang / Kenneth Gable / Sita D Gupta / Niranjanakumari Somashekarappa / Gongshe Han / Hongtu Zhao / Alexander G Myasnikov / Ravi C Kalathur / Teresa M Dunn / Chia-Hsueh Lee / ![]() ![]() Abstract: Sphingolipids are essential lipids in eukaryotic membranes. In humans, the first and rate-limiting step of sphingolipid synthesis is catalyzed by the serine palmitoyltransferase holocomplex, which ...Sphingolipids are essential lipids in eukaryotic membranes. In humans, the first and rate-limiting step of sphingolipid synthesis is catalyzed by the serine palmitoyltransferase holocomplex, which consists of catalytic components (SPTLC1 and SPTLC2) and regulatory components (ssSPTa and ORMDL3). However, the assembly, substrate processing and regulation of the complex are unclear. Here, we present 8 cryo-electron microscopy structures of the human serine palmitoyltransferase holocomplex in various functional states at resolutions of 2.6-3.4 Å. The structures reveal not only how catalytic components recognize the substrate, but also how regulatory components modulate the substrate-binding tunnel to control enzyme activity: ssSPTa engages SPTLC2 and shapes the tunnel to determine substrate specificity. ORMDL3 blocks the tunnel and competes with substrate binding through its amino terminus. These findings provide mechanistic insights into sphingolipid biogenesis governed by the serine palmitoyltransferase complex. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.7 KB | Display | ![]() |
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PDB format | ![]() | 160.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 971 KB | Display | ![]() |
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Full document | ![]() | 978.9 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 22608MC ![]() 7k0iC ![]() 7k0jC ![]() 7k0kC ![]() 7k0lC ![]() 7k0mC ![]() 7k0nC ![]() 7k0oC ![]() 7k0pC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Serine palmitoyltransferase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 52806.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 63004.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 8471.095 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 17512.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/VRP.gif)
![](data/chem/img/VRP.gif)
#5: Chemical | ChemComp-PLP / |
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#6: Chemical | ChemComp-VRP / |
-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 |
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Sample preparation
Component | Name: human serine palmitoyltransferase complexes / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
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: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70.67 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191726 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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