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- PDB-7k0k: Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa, 3... -

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Basic information

Entry
Database: PDB / ID: 7k0k
TitleHuman serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa, 3KS-bound
Components
  • Serine palmitoyltransferase 1Serine C-palmitoyltransferase
  • Serine palmitoyltransferase 2Serine C-palmitoyltransferase
  • Serine palmitoyltransferase small subunit ASerine C-palmitoyltransferase
KeywordsMEMBRANE PROTEIN / Sphingolipid
Function / homology
Function and homology information


sphinganine biosynthetic process / serine C-palmitoyltransferase complex / regulation of fat cell apoptotic process / sphingomyelin biosynthetic process / serine C-palmitoyltransferase / serine C-palmitoyltransferase activity / SPOTS complex / sphingosine biosynthetic process / sphingolipid biosynthetic process / ceramide biosynthetic process ...sphinganine biosynthetic process / serine C-palmitoyltransferase complex / regulation of fat cell apoptotic process / sphingomyelin biosynthetic process / serine C-palmitoyltransferase / serine C-palmitoyltransferase activity / SPOTS complex / sphingosine biosynthetic process / sphingolipid biosynthetic process / ceramide biosynthetic process / positive regulation of lipophagy / sphingolipid metabolic process / adipose tissue development / protein localization / pyridoxal phosphate binding / endoplasmic reticulum membrane / endoplasmic reticulum / integral component of membrane / cytoplasm
Small subunit of serine palmitoyltransferase-like / Pyridoxal phosphate-dependent transferase / Pyridoxal phosphate-dependent transferase domain 1 / Pyridoxal phosphate-dependent transferase, major domain / Aminotransferase, class I/classII / Aminotransferase, class-II, pyridoxal-phosphate binding site
Serine palmitoyltransferase 1 / Serine palmitoyltransferase 2 / Serine palmitoyltransferase small subunit A
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang, Y. / Niu, Y. / Zhang, Z. / Zhao, H. / Myasnikov, A. / Kalathur, R. / Lee, C.H.
CitationJournal: Nat Struct Mol Biol / Year: 2021
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Structure visualization

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Assembly

Deposited unit
A: Serine palmitoyltransferase 1
B: Serine palmitoyltransferase 2
C: Serine palmitoyltransferase small subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8295
Polymers124,2823
Non-polymers5472
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12510 Å2
ΔGint-85 kcal/mol
Surface area35520 Å2

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Components

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


Mass: 52806.770 Da / Num. of mol.: 1
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 / Serine C-palmitoyltransferase / 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
#3: Protein Serine palmitoyltransferase small subunit A / Serine C-palmitoyltransferase / Small subunit of serine palmitoyltransferase A / ssSPTa


Mass: 8471.095 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
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VSD / 3-Dehydrosphinganine / (2S,6E)-2-amino-1-hydroxyoctadec-6-en-3-one


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
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: human serine palmitoyltransferase complexes / Type: COMPLEX / Entity ID: #1-#3 / 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 FIELDBright-field microscopy
Image recordingElectron dose: 80.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133308 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067771
ELECTRON MICROSCOPYf_angle_d0.65610498
ELECTRON MICROSCOPYf_dihedral_angle_d22.2792897
ELECTRON MICROSCOPYf_chiral_restr0.0451157
ELECTRON MICROSCOPYf_plane_restr0.0041347

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