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- EMDB-22602: Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/OR... -

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Basic information

Entry
Database: EMDB / ID: EMD-22602
TitleHuman serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 1
Map dataSharpened_map
Sample
  • Complex: human serine palmitoyltransferase complexes
    • Protein or peptide: Serine palmitoyltransferase 1
  • Protein or peptide: Serine palmitoyltransferase 2
  • Protein or peptide: Serine palmitoyltransferase small subunit A
  • Protein or peptide: ORM1-like protein 3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsSphingolipid / MEMBRANE PROTEIN
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 / sphingolipid metabolic process / sphingolipid biosynthetic process / regulation of smooth muscle contraction / Sphingolipid de novo biosynthesis / ceramide biosynthetic process / positive regulation of lipophagy / negative regulation of B cell apoptotic process / motor behavior / adipose tissue development / specific granule membrane / myelination / positive regulation of autophagy / secretory granule membrane / positive regulation of protein localization to nucleus / pyridoxal phosphate binding / intracellular protein localization / 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
Serine palmitoyltransferase 1 / Serine palmitoyltransferase 2 / ORM1-like protein 3 / Serine palmitoyltransferase small subunit A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang Y / Niu Y
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.
History
DepositionSep 4, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing 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-7k0m
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22602.png

Downloads & links

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Map

FileDownload / File: emd_22602.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened_map
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-4.1511927 - 5.9264727
Average (Standard dev.)0.00048447095 (±0.12064046)
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-4.1515.9260.000

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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
Components
  • Complex: human serine palmitoyltransferase complexes
    • Protein or peptide: Serine palmitoyltransferase 1
  • Protein or peptide: Serine palmitoyltransferase 2
  • Protein or peptide: Serine palmitoyltransferase small subunit A
  • Protein or peptide: ORM1-like protein 3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: human serine palmitoyltransferase complexes

SupramoleculeName: human serine palmitoyltransferase complexes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine palmitoyltransferase 1

MacromoleculeName: Serine palmitoyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.80677 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATATEQWVL VEMVQALYEA PAYHLILEGI LILWIIRLLF SKTYKLQERS DLTVKEKEEL IEEWQPEPLV PPVPKDHPAL NYNIVSGPP SHKTVVNGKE CINFASFNFL GLLDNPRVKA AALASLKKYG VGTCGPRGFY GTFDVHLDLE DRLAKFMKTE E AIIYSYGF ...String:
MATATEQWVL VEMVQALYEA PAYHLILEGI LILWIIRLLF SKTYKLQERS DLTVKEKEEL IEEWQPEPLV PPVPKDHPAL NYNIVSGPP SHKTVVNGKE CINFASFNFL GLLDNPRVKA AALASLKKYG VGTCGPRGFY GTFDVHLDLE DRLAKFMKTE E AIIYSYGF ATIASAIPAY SKRGDIVFVD RAACFAIQKG LQASRSDIKL FKHNDMADLE RLLKEQEIED QKNPRKARVT RR FIVVEGL YMNTGTICPL PELVKLKYKY KARIFLEESL SFGVLGEHGR GVTEHYGINI DDIDLISANM ENALASIGGF CCG RSFVID HQRLSGQGYC FSASLPPLLA AAAIEALNIM EENPGIFAVL KEKCGQIHKA LQGISGLKVV GESLSPAFHL QLEE STGSR EQDVRLLQEI VDQCMNRSIA LTQARYLEKE EKCLPPPSIR VVVTVEQTEE ELERAASTIK EVAQAVLL

UniProtKB: Serine palmitoyltransferase 1

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Macromolecule #2: Serine palmitoyltransferase 2

MacromoleculeName: Serine palmitoyltransferase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.08002 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ NGGLYKRPFN EAFEETPMLV AVLTYVGYGV LTLFGYLRD FLRYWRIEKC HHATEREEQK DFVSLYQDFE NFYTRNLYMR IRDNWNRPIC SVPGARVDIM ERQSHDYNWS F KYTGNIIK ...String:
MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ NGGLYKRPFN EAFEETPMLV AVLTYVGYGV LTLFGYLRD FLRYWRIEKC HHATEREEQK DFVSLYQDFE NFYTRNLYMR IRDNWNRPIC SVPGARVDIM ERQSHDYNWS F KYTGNIIK GVINMGSYNY LGFARNTGSC QEAAAKVLEE YGAGVCSTRQ EIGNLDKHEE LEELVARFLG VEAAMAYGMG FA TNSMNIP ALVGKGCLIL SDELNHASLV LGARLSGATI RIFKHNNMQS LEKLLKDAIV YGQPRTRRPW KKILILVEGI YSM EGSIVR LPEVIALKKK YKAYLYLDEA HSIGALGPTG RGVVEYFGLD PEDVDVMMGT FT(LLP)SFGASGG YIGGKKELID YLRTHSHSA VYATSLSPPV VEQIITSMKC IMGQDGTSLG KECVQQLAEN TRYFRRRLKE MGFIIYGNED SPVVPLMLYM P AKIGAFGR EMLKRNIGVV VVGFPATPII ESRARFCLSA AHTKEILDTA LKEIDEVGDL LQLKYSRHRL

UniProtKB: Serine palmitoyltransferase 2

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Macromolecule #3: Serine palmitoyltransferase small subunit A

MacromoleculeName: Serine palmitoyltransferase small subunit A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.471095 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAGMALARAW KQMSWFYYQY LLVTALYMLE PWERTVFNSM LVSIVGMALY TGYVFMPQHI MAILHYFEIV Q

UniProtKB: Serine palmitoyltransferase small subunit A

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Macromolecule #4: ORM1-like protein 3

MacromoleculeName: ORM1-like protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.512594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MNVGTAHSEV NPNTRVMNSR GIWLSYVLAI GLLHIVLLSI PFVSVPVVWT LTNLIHNMGM YIFLHTVKGT PFETPDQGKA RLLTHWEQM DYGVQFTASR KFLTITPIVL YFLTSFYTKY DQIHFVLNTV SLMSVLIPKL PQLHGVRIFG INKY

UniProtKB: ORM1-like protein 3

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 14 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.53 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 169428
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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