+Open data
-Basic information
Entry | Database: PDB / ID: 5kdi | ||||||||||||
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Title | How FAPP2 Selects Simple Glycosphingolipids Using the GLTP-fold | ||||||||||||
Components | Pleckstrin homology domain-containing family A member 8 | ||||||||||||
Keywords | LIPID TRANSPORT / GLTP-fold / lipid transfer | ||||||||||||
Function / homology | Function and homology information glycolipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / ceramide binding / intermembrane lipid transfer / phosphatidylinositol biosynthetic process / phosphatidylinositol-4-phosphate binding ...glycolipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / ceramide binding / intermembrane lipid transfer / phosphatidylinositol biosynthetic process / phosphatidylinositol-4-phosphate binding / lipid transport / Synthesis of PIPs at the plasma membrane / trans-Golgi network / protein transport / Golgi membrane / Golgi apparatus / nucleoplasm / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Ochoa-Lizarralde, B. / Popov, A.N. / Samygina, V.R. / Patel, D.J. / Brown, R.E. / Malinina, L. | ||||||||||||
Funding support | United States, Spain, Russian Federation, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2018 Title: Structural analyses of 4-phosphate adaptor protein 2 yield mechanistic insights into sphingolipid recognition by the glycolipid transfer protein family. Authors: Ochoa-Lizarralde, B. / Gao, Y.G. / Popov, A.N. / Samygina, V.R. / Zhai, X. / Mishra, S.K. / Boldyrev, I.A. / Molotkovsky, J.G. / Simanshu, D.K. / Patel, D.J. / Brown, R.E. / Malinina, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kdi.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdi.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdi ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdi | HTTPS FTP |
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-Related structure data
Related structure data | 2eukS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23489.021 Da / Num. of mol.: 2 / Mutation: E377A, E378K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHA8, FAPP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JA3 #2: Chemical | #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: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion / Details: 13-15% PEG8000, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→15 Å / Num. obs: 78300 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.754 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EUK Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.32 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.51 Å2 / Biso mean: 24.523 Å2 / Biso min: 10.64 Å2
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Refinement step | Cycle: final / Resolution: 1.45→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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