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- PDB-4kf6: Crystal structure of human ceramide-1-phosphate transfer protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kf6 | ||||||
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Title | Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 8:0 Ceramide-1-Phosphate (8:0-C1P) | ||||||
![]() | Glycolipid transfer protein domain-containing protein 1 | ||||||
![]() | LIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid | ||||||
Function / homology | ![]() ceramide 1-phosphate transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...ceramide 1-phosphate transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy / phospholipid binding / endosome membrane / Golgi apparatus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Simanshu, D.K. / Brown, R.E. / Patel, D.J. | ||||||
![]() | ![]() Title: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids. Authors: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 502.1 KB | Display | ![]() |
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PDB format | ![]() | 418.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k80C ![]() 4k84C ![]() 4k85C ![]() 4k8nC ![]() 4kbrC ![]() 4kbsC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24484.154 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-1T9 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2009 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 25734 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 83.28 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 251.39 Å2 / Biso mean: 81.1491 Å2 / Biso min: 25.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.195→38.827 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -23.4021 Å / Origin y: 2.5709 Å / Origin z: 24.0531 Å
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Refinement TLS group |
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