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- PDB-2e3o: Crystal structure of CERT START domain in complex with C16-cerami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2e3o | ||||||
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Title | Crystal structure of CERT START domain in complex with C16-ceramide (P212121) | ||||||
![]() | Lipid-transfer protein CERT | ||||||
![]() | LIPID TRANSPORT / LIPID TRANSFER PROTEIN / CERT / CERAMIDE TRANSFER | ||||||
Function / homology | ![]() intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / response to endoplasmic reticulum stress / mitochondrion organization / muscle contraction / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kudo, N. / Kumagai, K. / Wakatsuki, S. / Nishijima, M. / Hanada, K. / Kato, R. | ||||||
![]() | ![]() Title: Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Authors: Kudo, N. / Kumagai, K. / Tomishige, N. / Yamaji, T. / Wakatsuki, S. / Nishijima, M. / Hanada, K. / Kato, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 49.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 724.2 KB | Display | ![]() |
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Full document | ![]() | 727.2 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e3mC ![]() 2e3nC ![]() 2e3pC ![]() 2e3qC ![]() 2e3rC ![]() 2e3sC ![]() 2z9yC ![]() 2z9zC 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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Unit cell |
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Components
#1: Protein | Mass: 28931.764 Da / Num. of mol.: 1 / Fragment: CERT START DOMAIN (RESIDUES 347-598) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-16C / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 41548 / % possible obs: 99.1 % |
Reflection shell | Resolution: 1.55→1.61 Å / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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