2E3P

Crystal structure of CERT START domain in complex with C16-cearmide (P1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.

Kudo, N.Kumagai, K.Tomishige, N.Yamaji, T.Wakatsuki, S.Nishijima, M.Hanada, K.Kato, R.

(2008) Proc.Natl.Acad.Sci.Usa 105: 488-493

  • DOI: 10.1073/pnas.0709191105
  • Primary Citation of Related Structures:  2E3M, 2E3N, 2E3O, 2E3Q, 2E3R, 2E3S, 2Z9Y, 2Z9Z

  • PubMed Abstract: 
  • In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic 68-kDa protein wi ...

    In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic 68-kDa protein with a C-terminal steroidogenic acute regulatory protein-related lipid transfer (START) domain. The CERT START domain efficiently transfers natural D-erythro-C16-ceramide, but not lipids with longer (C20) amide-acyl chains. The molecular mechanisms of ceramide specificity, both stereo-specific recognition and length limit, are not well understood. Here we report the crystal structures of the CERT START domain in its apo-form and in complex with ceramides having different acyl chain lengths. In these complex structures, one ceramide molecule is buried in a long amphiphilic cavity. At the far end of the cavity, the amide and hydroxyl groups of ceramide form a hydrogen bond network with specific amino acid residues that play key roles in stereo-specific ceramide recognition. At the head of the ceramide molecule, there is no extra space to accommodate additional bulky groups. The two aliphatic chains of ceramide are surrounded by the hydrophobic wall of the cavity, whose size and shape dictate the length limit for cognate ceramides. Furthermore, local high-crystallographic B-factors suggest that the alpha-3 and the Omega1 loop might work as a gate to incorporate the ceramide into the cavity. Thus, the structures demonstrate the structural basis for the mechanism by which CERT can distinguish ceramide from other lipid types yet still recognize multiple species of ceramides.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipid-transfer protein CERT
A, B
255Homo sapiensGene Names: COL4A3BP (CERT, STARD11)
Find proteins for Q9Y5P4 (Homo sapiens)
Go to Gene View: COL4A3BP
Go to UniProtKB:  Q9Y5P4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16C
Query on 16C

Download SDF File 
Download CCD File 
A, B
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
C16-CERAMIDE, N-PALMITOYL-D-ERYTHRO-SPHINGOSINE, (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL, (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL
C34 H67 N O3
YDNKGFDKKRUKPY-TURZORIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.976α = 77.72
b = 49.699β = 71.06
c = 62.365γ = 82.10
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance