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Yorodumi- PDB-4k8n: Crystal structure of human ceramide-1-phosphate transfer protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k8n | ||||||
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Title | Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 18:1 Ceramide-1-Phosphate (18:1-C1P) | ||||||
Components | Glycolipid transfer protein domain-containing protein 1 | ||||||
Keywords | LIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid | ||||||
Function / homology | Function and homology information ceramide 1-phosphate transport / Glycosphingolipid biosynthesis / ceramide transport / glycosphingolipid biosynthetic process / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production ...ceramide 1-phosphate transport / Glycosphingolipid biosynthesis / ceramide transport / glycosphingolipid biosynthetic process / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å | ||||||
Authors | Simanshu, D.K. / Brown, R.E. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k8n.cif.gz | 504.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k8n.ent.gz | 425.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k8n ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k8n | HTTPS FTP |
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-Related structure data
Related structure data | 4k80C 4k84C 4k85C 4kbrC 4kbsC 4kf6C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: GLTPD1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q5TA50 #2: Chemical | ChemComp-1Q0 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium malonate, 0.1 M Bis-Tris Propane pH 6.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→30 Å / Num. obs: 35765 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CPTP in complex with 2:0 ceramide-1-phosphate Resolution: 3.102→30.052 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.35 / Phase error: 29.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.3277 Å2
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Refinement step | Cycle: LAST / Resolution: 3.102→30.052 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 38.5333 Å / Origin y: -63.1682 Å / Origin z: -3.6328 Å
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Refinement TLS group | Selection details: all |