9EOT | pdb_00009eot

Structure of human ceramide synthase 6 (CerS6) bound to C16:0 (nanobody Nb02)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EOT

This is version 1.2 of the entry. See complete history

Literature

Structural basis of the mechanism and inhibition of a human ceramide synthase.

Pascoa, T.C.Pike, A.C.W.Tautermann, C.S.Chi, G.Traub, M.Quigley, A.Chalk, R.Stefanic, S.Thamm, S.Pautsch, A.Carpenter, E.P.Schnapp, G.Sauer, D.B.

(2025) Nat Struct Mol Biol 32: 431-440

  • DOI: https://doi.org/10.1038/s41594-024-01414-3
  • Primary Citation Related Structures: 
    8QZ6, 8QZ7, 9EOT

  • PubMed Abstract: 

    Ceramides are bioactive sphingolipids crucial for regulating cellular metabolism. Ceramides and dihydroceramides are synthesized by six ceramide synthase (CerS) enzymes, each with specificity for different acyl-CoA substrates. Ceramide with a 16-carbon acyl chain (C16 ceramide) has been implicated in obesity, insulin resistance and liver disease and the C16 ceramide-synthesizing CerS6 is regarded as an attractive drug target for obesity-associated disease. Despite their importance, the molecular mechanism underlying ceramide synthesis by CerS enzymes remains poorly understood. Here we report cryo-electron microscopy structures of human CerS6, capturing covalent intermediate and product-bound states. These structures, along with biochemical characterization, reveal that CerS catalysis proceeds through a ping-pong reaction mechanism involving a covalent acyl-enzyme intermediate. Notably, the product-bound structure was obtained upon reaction with the mycotoxin fumonisin B1, yielding insights into its inhibition of CerS. These results provide a framework for understanding CerS function, selectivity and inhibition and open routes for future drug discovery.


  • Organizational Affiliation
    • Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK. tomas.pascoa@cmd.ox.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 117.04 kDa 
  • Atom Count: 7,214 
  • Modeled Residue Count: 904 
  • Deposited Residue Count: 982 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Ceramide synthase 6A,
D [auth C]
357Homo sapiensMutation(s): 0 
Gene Names: CERS6LASS6
EC: 2.3.1.291 (PDB Primary Data), 2.3.1 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMG9 (Homo sapiens)
Explore Q6ZMG9 
Go to UniProtKB:  Q6ZMG9
PHAROS:  Q6ZMG9
GTEx:  ENSG00000172292 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZMG9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q6ZMG9-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody-02B,
C [auth D]
134Vicugna pacosMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1

Query on PC1



Download:Ideal Coordinates CCD File
F [auth A],
I [auth C]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PLM
(Subject of Investigation/LOI)

Query on PLM



Download:Ideal Coordinates CCD File
E [auth A],
H [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
J [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102164/B/15/Z
Wellcome TrustUnited Kingdom106169/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-26
    Changes: Data collection, Database references