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- PDB-7cqk: Cryo-EM structure of the substrate-bound SPT-ORMDL3 complex -

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Basic information

Entry
Database: PDB / ID: 7cqk
TitleCryo-EM structure of the substrate-bound SPT-ORMDL3 complex
Components
  • (Serine palmitoyltransferase ...) x 3
  • ORM1-like protein 3
KeywordsTRANSFERASE / membrane protein / lipid synthesis
Function / homology
Function and homology information


sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / sphingosine biosynthetic process ...sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / sphingosine biosynthetic process / regulation of smooth muscle contraction / 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 / specific granule membrane / positive regulation of autophagy / myelination / secretory granule membrane / positive regulation of protein localization to nucleus / protein localization / pyridoxal phosphate binding / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
: / Small subunit of serine palmitoyltransferase-like / Small subunit of serine palmitoyltransferase-like / ORMDL family / ORMDL family / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II ...: / Small subunit of serine palmitoyltransferase-like / Small subunit of serine palmitoyltransferase-like / ORMDL family / ORMDL family / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-GE0 / Chem-PLS / Serine palmitoyltransferase 1 / Serine palmitoyltransferase 2 / ORM1-like protein 3 / Serine palmitoyltransferase small subunit A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, S.S. / Xie, T. / Wang, L. / Gong, X.
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
Authors: Sisi Li / Tian Xie / Peng Liu / Lei Wang / Xin Gong /
Abstract: Human serine palmitoyltransferase (SPT) complex catalyzes the initial and rate-limiting step in the de novo biosynthesis of all sphingolipids. ORMDLs regulate SPT function, with human ORMDL3 being ...Human serine palmitoyltransferase (SPT) complex catalyzes the initial and rate-limiting step in the de novo biosynthesis of all sphingolipids. ORMDLs regulate SPT function, with human ORMDL3 being related to asthma. Here we report three high-resolution cryo-EM structures: the human SPT complex, composed of SPTLC1, SPTLC2 and SPTssa; the SPT-ORMDL3 complex; and the SPT-ORMDL3 complex bound to two substrates, PLP-L-serine (PLS) and a non-reactive palmitoyl-CoA analogue. SPTLC1 and SPTLC2 form a dimer of heterodimers as the catalytic core. SPTssa participates in acyl-CoA coordination, thereby stimulating the SPT activity and regulating the substrate selectivity. ORMDL3 is located in the center of the complex, serving to stabilize the SPT assembly. Our structural and biochemical analyses provide a molecular basis for the assembly and substrate selectivity of the SPT and SPT-ORMDL3 complexes, and lay a foundation for mechanistic understanding of sphingolipid homeostasis and for related therapeutic drug development.
History
DepositionAug 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
S: Serine palmitoyltransferase 1
T: Serine palmitoyltransferase 2
A: ORM1-like protein 3
E: Serine palmitoyltransferase small subunit A
C: Serine palmitoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,2297
Polymers196,8735
Non-polymers1,3562
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Serine palmitoyltransferase ... , 3 types, 4 molecules SCTE

#1: Protein Serine palmitoyltransferase 1 / Long chain base biosynthesis protein 1 / LCB 1 / Serine-palmitoyl-CoA transferase 1 / SPT1


Mass: 52806.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTLC1, LCB1 / Production host: Homo sapiens (human) / References: UniProt: O15269, serine C-palmitoyltransferase
#2: Protein Serine palmitoyltransferase 2 / Long chain base biosynthesis protein 2 / LCB 2 / Long chain base biosynthesis protein 2a / LCB2a / ...Long chain base biosynthesis protein 2 / LCB 2 / Long chain base biosynthesis protein 2a / LCB2a / Serine-palmitoyl-CoA transferase 2 / SPT 2


Mass: 63004.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTLC2, KIAA0526, LCB2 / Production host: Homo sapiens (human) / References: UniProt: O15270, serine C-palmitoyltransferase
#4: Protein Serine palmitoyltransferase small subunit A / Small subunit of serine palmitoyltransferase A / ssSPTa


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 / Production host: Homo sapiens (human) / References: UniProt: Q969W0

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Protein , 1 types, 1 molecules A

#3: Protein ORM1-like protein 3


Mass: 17512.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORMDL3 / Production host: Homo sapiens (human) / References: UniProt: Q8N138

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O8P
#6: Chemical ChemComp-GE0 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(2-oxidanylideneheptadecylsulfanyl)ethylamino]propyl]amino]butyl] hydrogen phosphate


Mass: 1019.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H68N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: membrane protein 5 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106196 / Symmetry type: POINT

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