[English] 日本語
Yorodumi- PDB-4k84: Crystal structure of human ceramide-1-phosphate transfer protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k84 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 16:0 ceramide-1-phosphate (16:0-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 / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / 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 transfer activity / ceramide 1-phosphate binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.897 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k84.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k84.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k84_validation.pdf.gz | 811.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4k84_full_validation.pdf.gz | 820 KB | Display | |
Data in XML | 4k84_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4k84_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k84 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k84 | HTTPS FTP |
-Related structure data
Related structure data | 4k80C 4k85C 4k8nC 4kbrC 4kbsC 4kf6C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24484.154 Da / Num. of mol.: 2 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 | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.18 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M MMT buffer pH 5.0, 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2398 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 30620 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human ceramide-1-phosphate transfer protein in complex with C2 Ceramide-1-phosphate (2:0 C1P) Resolution: 1.897→40.278 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.2 / σ(F): 0.11 / Phase error: 22.43 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.821 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→40.278 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|