5JJD

crystal structure of the ceramide transfer protein PH and START domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain.

Prashek, J.Bouyain, S.Fu, M.Li, Y.Berkes, D.Yao, X.

(2017) J. Biol. Chem. 292: 14217-14228

  • DOI: 10.1074/jbc.M117.780007

  • PubMed Abstract: 
  • <i>De novo </i> synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology ( ...

    De novo synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology (PH) domain targets it to the Golgi by binding to phosphatidylinositol 4-phosphate (PtdIns(4)P) in the Golgi membrane, whereas its C-terminal StAR-related lipid transfer domain (START) carries out ceramide transfer. Hyperphosphorylation of a serine-rich motif immediately after the PH domain decreases both PtdIns(4)P binding and ceramide transfer by CERT. This down-regulation requires both the PH and START domains, suggesting a possible inhibitory interaction between the two domains. In this study we show that isolated PH and START domains interact with each other. The crystal structure of a PH-START complex revealed that the START domain binds to the PH domain at the same site for PtdIns(4)P-binding, suggesting that the START domain competes with PtdIns(4)P for association with the PH domain. We further report that mutations disrupting the PH-START interaction increase both PtdIns(4)P-binding affinity and ceramide transfer activity of a CERT-serine-rich phosphorylation mimic. We also found that these mutations increase the Golgi localization of CERT inside the cell, consistent with enhanced PtdIns(4)P binding of the mutant. Collectively, our structural, biochemical, and cellular investigations provide important structural insight into the regulation of CERT function and localization.


    Organizational Affiliation

    From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110.,the Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, and.,From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, yaoxia@umkc.edu.,the Department of Organic Chemistry, Slovak University of Technology in Bratislava, Radlinského 9, 81237 Bratislava, Slovakia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen type IV alpha-3-binding protein
A
106Homo sapiensMutation(s): 0 
Gene Names: CERT (COL4A3BP, STARD11)
Find proteins for Q9Y5P4 (Homo sapiens)
Go to UniProtKB:  Q9Y5P4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Collagen type IV alpha-3-binding protein
B
246Homo sapiensMutation(s): 0 
Gene Names: CERT (COL4A3BP, STARD11)
Find proteins for Q9Y5P4 (Homo sapiens)
Go to UniProtKB:  Q9Y5P4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.761α = 90.00
b = 60.914β = 90.00
c = 95.804γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1 R15 GM113200-01

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references