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- EMDB-22604: Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/OR... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-22604
TitleHuman serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 2
Map data
Samplehuman serine palmitoyltransferase complexes
  • (Serine palmitoyltransferase ...Serine C-palmitoyltransferase) x 3
  • ORM1-like protein 3
  • (ligand) x 2
Function / homology
Function and homology information


negative regulation of serine C-palmitoyltransferase activity / negative regulation of ceramide biosynthetic process / cellular sphingolipid homeostasis / sphinganine biosynthetic process / regulation of fat cell apoptotic process / serine C-palmitoyltransferase complex / sphingomyelin biosynthetic process / SPOTS complex / serine C-palmitoyltransferase / serine C-palmitoyltransferase activity ...negative regulation of serine C-palmitoyltransferase activity / negative regulation of ceramide biosynthetic process / cellular sphingolipid homeostasis / sphinganine biosynthetic process / regulation of fat cell apoptotic process / serine C-palmitoyltransferase complex / sphingomyelin biosynthetic process / SPOTS complex / serine C-palmitoyltransferase / serine C-palmitoyltransferase activity / regulation of smooth muscle contraction / sphingosine biosynthetic process / sphingolipid biosynthetic process / ceramide biosynthetic process / ceramide metabolic process / positive regulation of lipophagy / sphingolipid metabolic process / motor behavior / negative regulation of B cell apoptotic process / myelination / adipose tissue development / specific granule membrane / positive regulation of autophagy / secretory granule membrane / protein localization / positive regulation of protein localization to nucleus / pyridoxal phosphate binding / endoplasmic reticulum membrane / neutrophil degranulation / endoplasmic reticulum / integral component of membrane / plasma membrane / cytoplasm
ORM1-like protein 3 / Small subunit of serine palmitoyltransferase-like / Pyridoxal phosphate-dependent transferase / Pyridoxal phosphate-dependent transferase domain 1 / Pyridoxal phosphate-dependent transferase, major domain / ORMDL family / Aminotransferase, class I/classII / Aminotransferase, class-II, pyridoxal-phosphate binding site
Serine palmitoyltransferase 1 / Serine palmitoyltransferase 2 / ORM1-like protein 3 / Serine palmitoyltransferase small subunit A
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang Y / Niu Y / Zhang Z / Zhao H / Myasnikov A / Kalathur R / Lee CH
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 ReportSummary, Full report, XML, About validation report
History
DepositionSep 4, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateMar 24, 2021-
Current statusMar 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k0n
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22604.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 352 pix.
= 353.76 Å
1.01 Å/pix.
x 352 pix.
= 353.76 Å
1.01 Å/pix.
x 352 pix.
= 353.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-3.069672 - 5.030576
Average (Standard dev.)0.0006076498 (±0.10337686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 353.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0051.0051.005
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z353.760353.760353.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-3.0705.0310.001

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Supplemental data

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Sample components

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Entire human serine palmitoyltransferase complexes

EntireName: human serine palmitoyltransferase complexes / Number of components: 7

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Component #1: protein, human serine palmitoyltransferase complexes

ProteinName: human serine palmitoyltransferase complexes / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Serine palmitoyltransferase 1

ProteinName: Serine palmitoyltransferase 1Serine C-palmitoyltransferase
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 52.80677 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Serine palmitoyltransferase 2

ProteinName: Serine palmitoyltransferase 2Serine C-palmitoyltransferase
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 63.00416 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Serine palmitoyltransferase small subunit A

ProteinName: Serine palmitoyltransferase small subunit ASerine C-palmitoyltransferase
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.471095 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, ORM1-like protein 3

ProteinName: ORM1-like protein 3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.512594 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: ligand, PYRIDOXAL-5'-PHOSPHATE

LigandName: PYRIDOXAL-5'-PHOSPHATEPyridoxal phosphate / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.247142 kDa

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Component #7: ligand, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propy...

LigandName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.760076 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 72.53 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 195572
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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