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- PDB-4k80: 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: 4k80 | ||||||
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Title | Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 2:0 ceramide-1-phosphate (2:0-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 transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / 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 transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / 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 | ![]() | 61.4 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 612.4 KB | Display | ![]() |
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Full document | ![]() | 613.2 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k84C ![]() 4k85C ![]() 4k8nC ![]() 4kbrC ![]() 4kbsC ![]() 4kf6C 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24484.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-1PW / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG3350, 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 |
Diffraction measurement | Details: 1.00 degrees, 10.0 sec, detector distance 204.82 mm |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.072 / Number: 178254 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 20690 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 32.169 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.079 / Rsym value: 0.495 / % possible all: 100 |
Cell measurement | Reflection used: 178254 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CPTP in complex with C8 ceramide -1-phosphate Resolution: 2.051→28.144 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8823 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 17.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.046 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.11 Å2 / Biso mean: 32.1221 Å2 / Biso min: 18.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.051→28.144 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: 7
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