4KF6 | pdb_00004kf6

Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 8:0 Ceramide-1-Phosphate (8:0-C1P)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 ?
  • R-Value Free: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids.

Simanshu, D.K.Kamlekar, R.K.Wijesinghe, D.S.Zou, X.Zhai, X.Mishra, S.K.Molotkovsky, J.G.Malinina, L.Hinchcliffe, E.H.Chalfant, C.E.Brown, R.E.Patel, D.J.

(2013) Nature 500: 463-467

  • DOI: https://doi.org/10.1038/nature12332
  • Primary Citation of Related Structures:  
    4K80, 4K84, 4K85, 4K8N, 4KBR, 4KBS, 4KF6

  • PubMed Abstract: 

    Phosphorylated sphingolipids ceramide-1-phosphate (C1P) and sphingosine-1-phosphate (S1P) have emerged as key regulators of cell growth, survival, migration and inflammation. C1P produced by ceramide kinase is an activator of group IVA cytosolic phospholipase A2¦Á (cPLA2¦Á), the rate-limiting releaser of arachidonic acid used for pro-inflammatory eicosanoid production, which contributes to disease pathogenesis in asthma or airway hyper-responsiveness, cancer, atherosclerosis and thrombosis. To modulate eicosanoid action and avoid the damaging effects of chronic inflammation, cells require efficient targeting, trafficking and presentation of C1P to specific cellular sites. Vesicular trafficking is likely but non-vesicular mechanisms for C1P sensing, transfer and presentation remain unexplored. Moreover, the molecular basis for selective recognition and binding among signalling lipids with phosphate headgroups, namely C1P, phosphatidic acid or their lyso-derivatives, remains unclear. Here, a ubiquitously expressed lipid transfer protein, human GLTPD1, named here CPTP, is shown to specifically transfer C1P between membranes. Crystal structures establish C1P binding through a novel surface-localized, phosphate headgroup recognition centre connected to an interior hydrophobic pocket that adaptively expands to ensheath differing-length lipid chains using a cleft-like gating mechanism. The two-layer, ¦Á-helically-dominated 'sandwich' topology identifies CPTP as the prototype for a new glycolipid transfer protein fold subfamily. CPTP resides in the cell cytosol but associates with the trans-Golgi network, nucleus and plasma membrane. RNA interference-induced CPTP depletion elevates C1P steady-state levels and alters Golgi cisternae stack morphology. The resulting C1P decrease in plasma membranes and increase in the Golgi complex stimulates cPLA2¦Á release of arachidonic acid, triggering pro-inflammatory eicosanoid generation.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycolipid transfer protein domain-containing protein 1
A, B, C, D, E
A, B, C, D, E, F
215Homo sapiensMutation(s): 0 
Gene Names: GLTPD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TA50 (Homo sapiens)
Explore Q5TA50 
Go to UniProtKB:  Q5TA50
PHAROS:  Q5TA50
GTEx:  ENSG00000224051 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TA50
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 ?
  • R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 81.884¦Á = 90
b = 122.399¦Â = 90
c = 149.99¦Ã = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations
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