7K0N

Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the regulation of human serine palmitoyltransferase complexes.

Wang, Y.Niu, Y.Zhang, Z.Gable, K.Gupta, S.D.Somashekarappa, N.Han, G.Zhao, H.Myasnikov, A.G.Kalathur, R.C.Dunn, T.M.Lee, C.H.

(2021) Nat Struct Mol Biol 28: 240-248

  • DOI: 10.1038/s41594-020-00551-9
  • Primary Citation of Related Structures:  
    7K0N, 7K0O, 7K0L, 7K0M, 7K0P, 7K0Q, 7K0J, 7K0K, 7K0I

  • PubMed 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 consists of catalytic components (SPTLC1 and SPTLC2) and regulatory components (ssSPTa and ORMDL3) ...

    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.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. ChiaHsueh.Lee@stjude.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine palmitoyltransferase 1A, G [auth E]473Homo sapiensMutation(s): 0 
Gene Names: SPTLC1LCB1
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15269 (Homo sapiens)
Explore O15269 
Go to UniProtKB:  O15269
PHAROS:  O15269
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine palmitoyltransferase 2B, H [auth F]562Homo sapiensMutation(s): 0 
Gene Names: SPTLC2KIAA0526LCB2
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15270 (Homo sapiens)
Explore O15270 
Go to UniProtKB:  O15270
PHAROS:  O15270
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Serine palmitoyltransferase small subunit AC, F [auth G]71Homo sapiensMutation(s): 0 
Gene Names: SPTSSAC14orf147SSSPTA
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q969W0 (Homo sapiens)
Explore Q969W0 
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PHAROS:  Q969W0
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ORM1-like protein 3D, E [auth H]153Homo sapiensMutation(s): 0 
Gene Names: ORMDL3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N138 (Homo sapiens)
Explore Q8N138 
Go to UniProtKB:  Q8N138
PHAROS:  Q8N138
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
J [auth B] , K [auth B] , L [auth C] , M [auth C] , N [auth C] , O [auth D] , P [auth D] , Q [auth D] , 
J [auth B],  K [auth B],  L [auth C],  M [auth C],  N [auth C],  O [auth D],  P [auth D],  Q [auth D],  R [auth H],  S [auth H],  T [auth H],  U [auth G],  V [auth G],  W [auth G],  X [auth F],  Y [auth F]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
I [auth B], Z [auth F]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references