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Yorodumi- PDB-6gqf: The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gqf | |||||||||
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Title | The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol | |||||||||
Components | GRAM domain-containing protein 1A | |||||||||
Keywords | LIPID TRANSPORT / cholesterol / plasma membrane / endoplasmic reticulum | |||||||||
Function / homology | Function and homology information : / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / cellular response to cholesterol / cholesterol transfer activity / cholesterol binding / autophagosome / extrinsic component of cytoplasmic side of plasma membrane / autophagy / cytoplasmic vesicle ...: / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / cellular response to cholesterol / cholesterol transfer activity / cholesterol binding / autophagosome / extrinsic component of cytoplasmic side of plasma membrane / autophagy / cytoplasmic vesicle / membrane => GO:0016020 / endoplasmic reticulum membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Fairall, L. / Gurnett, J.E. / Vashi, D. / Sandhu, J. / Tontonoz, P. / Schwabe, J.W.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell / Year: 2018 Title: Aster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian Cells. Authors: Sandhu, J. / Li, S. / Fairall, L. / Pfisterer, S.G. / Gurnett, J.E. / Xiao, X. / Weston, T.A. / Vashi, D. / Ferrari, A. / Orozco, J.L. / Hartman, C.L. / Strugatsky, D. / Lee, S.D. / He, C. / ...Authors: Sandhu, J. / Li, S. / Fairall, L. / Pfisterer, S.G. / Gurnett, J.E. / Xiao, X. / Weston, T.A. / Vashi, D. / Ferrari, A. / Orozco, J.L. / Hartman, C.L. / Strugatsky, D. / Lee, S.D. / He, C. / Hong, C. / Jiang, H. / Bentolila, L.A. / Gatta, A.T. / Levine, T.P. / Ferng, A. / Lee, R. / Ford, D.A. / Young, S.G. / Ikonen, E. / Schwabe, J.W.R. / Tontonoz, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gqf.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gqf.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/6gqf ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gqf | HTTPS FTP |
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-Related structure data
Related structure data | 5yqjS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25995.459 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gramd1a, D7Bwg0611e, Kiaa1533 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8VEF1 #2: Chemical | ChemComp-HC3 / #3: Chemical | ChemComp-GOL / |
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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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M NaCl, 0.1 M sodium cacodylate pH6, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→67.203 Å / Num. obs: 18439 / % possible obs: 99 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2958 / CC1/2: 0.891 / Rpim(I) all: 0.21 / Rrim(I) all: 0.662 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yqj Resolution: 2.9→67.203 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→67.203 Å
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Refine LS restraints |
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LS refinement shell |
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