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Yorodumi- PDB-2z9y: Crystal structure of CERT START domain in complex with C10-diacyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z9y | ||||||
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Title | Crystal structure of CERT START domain in complex with C10-diacylglycerol | ||||||
Components | Lipid-transfer protein CERT | ||||||
Keywords | LIPID TRANSPORT / LIPID TRANSFER PROTEIN / CERT / CERAMIDE TRANSFER | ||||||
Function / homology | Function and homology information intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis / lipid homeostasis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / heart morphogenesis / muscle contraction / response to endoplasmic reticulum stress / mitochondrion organization / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kudo, N. / Kumagai, K. / Wakatsuki, S. / Nishijima, M. / Hanada, K. / Kato, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z9y.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z9y.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z9y_validation.pdf.gz | 695.2 KB | Display | wwPDB validaton report |
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Full document | 2z9y_full_validation.pdf.gz | 696.8 KB | Display | |
Data in XML | 2z9y_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2z9y_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z9y ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z9y | HTTPS FTP |
-Related structure data
Related structure data | 2e3mC 2e3nSC 2e3oC 2e3pC 2e3qC 2e3rC 2e3sC 2z9zC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: CERT / Plasmid: PGEX-5X1 (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q53YV2, UniProt: Q9Y5P4*PLUS |
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#2: Chemical | ChemComp-DDR / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 21390 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 3.6 % / Num. unique all: 2058 / Rsym value: 0.37 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E3N Resolution: 1.8→39.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.197 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 36.919 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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