8Y2N

Cryo-EM structure of the apo Lac1-Lip1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Mechanism of ceramide synthase inhibition by fumonisin B 1.

Zhang, Z.Fang, Q.Xie, T.Gong, X.

(2024) Structure 32: 1419-1428.e4

  • DOI: https://doi.org/10.1016/j.str.2024.06.002
  • Primary Citation of Related Structures:  
    8Y2M, 8Y2N, 8ZB1

  • PubMed Abstract: 

    Ceramide synthases (CerSs) play crucial roles in sphingolipid metabolism and have emerged as promising drug targets for metabolic diseases, cancers, and antifungal therapy. However, the therapeutic targeting of CerSs has been hindered by a limited understanding of their inhibition mechanisms by small molecules. Fumonisin B 1 (FB 1 ) has been extensively studied as a potent inhibitor of eukaryotic CerSs. In this study, we characterize the inhibition mechanism of FB 1 on yeast CerS (yCerS) and determine the structures of both FB 1 -bound and N-acyl-FB 1 -bound yCerS. Through our structural analysis and the observation of N-acylation of FB 1 by yCerS, we propose a potential ping-pong catalytic mechanism for FB 1 N-acylation by yCerS. Lastly, we demonstrate that FB 1 exhibits lower binding affinity for yCerS compared to the C26- coenzyme A (CoA) substrate, suggesting that the potent inhibitory effect of FB 1 on yCerS may primarily result from the N-acyl-FB 1 catalyzed by yCerS, rather than through direct binding of FB 1 .


  • Organizational Affiliation

    Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ceramide synthase LAC1
A, C
428Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LAC1DGT1YKL008CYKL156
EC: 2.3.1.297
Membrane Entity: Yes 
UniProt
Find proteins for P28496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28496 
Go to UniProtKB:  P28496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28496
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ceramide synthase subunit LIP1
B, D
150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LIP1YMR298W
Membrane Entity: Yes 
UniProt
Find proteins for Q03579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03579 
Go to UniProtKB:  Q03579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03579
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PL
Query on 6PL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth C]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth C],
J [auth C],
K [auth D],
L [auth D]
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release