8IJR

The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 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

Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis.

Hu, K.Zhang, Q.Chen, Y.Yang, J.Xia, Y.Rao, B.Li, S.Shen, Y.Cao, M.Lu, H.Qin, A.Jiang, X.C.Yao, D.Zhao, J.Zhou, L.Cao, Y.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01237-2
  • Primary Citation of Related Structures:  
    8IJQ, 8IJR, 8W9W, 8W9Y

  • PubMed Abstract: 

    Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) family, comprising SMS1, SMS2 and SMS-related (SMSr) members. Although SMS1 and SMS2 exhibit SMS activity, SMSr possesses ceramide phosphoethanolamine synthase activity. Here we determined the cryo-electron microscopic structures of human SMSr in complexes with ceramide, diacylglycerol/phosphoethanolamine and ceramide/phosphoethanolamine (CPE). The structures revealed a hexameric arrangement with a reaction chamber located between the transmembrane helices. Within this structure, a catalytic pentad E-H/D-H-D was identified, situated at the interface between the lipophilic and hydrophilic segments of the reaction chamber. Additionally, the study unveiled the two-step synthesis process catalyzed by SMSr, involving PE-PLC (phosphatidylethanolamine-phospholipase C) hydrolysis and the subsequent transfer of the phosphoethanolamine moiety to ceramide. This research provides insights into the catalytic mechanism of SMSr and expands our understanding of sphingolipid metabolism.


  • Organizational Affiliation

    Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingomyelin synthase-related protein 1
A, B, C, D, E
A, B, C, D, E, F
415Homo sapiensMutation(s): 0 
Gene Names: SAMD8
EC: 2.7.8.27
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LT4 (Homo sapiens)
Explore Q96LT4 
Go to UniProtKB:  Q96LT4
PHAROS:  Q96LT4
GTEx:  ENSG00000156671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LT4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z0P (Subject of Investigation/LOI)
Query on Z0P

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
L [auth D]
M [auth E]
G [auth A],
I [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F]
(2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
C37 H70 O5
IIEPDWHEGOSXLD-NMYQGLQJSA-N
OPE (Subject of Investigation/LOI)
Query on OPE

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER
C2 H8 N O4 P
SUHOOTKUPISOBE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072468
National Natural Science Foundation of China (NSFC)China82272519

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references