+Open data
-Basic information
Entry | Database: PDB / ID: 5oyl | ||||||
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Title | VSV G CR2 | ||||||
Components |
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Keywords | VIRAL PROTEIN / c | ||||||
Function / homology | Function and homology information receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / low-density lipoprotein particle receptor activity / negative regulation of low-density lipoprotein particle clearance / Chylomicron clearance / response to caloric restriction / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / sorting endosome / lipoprotein particle binding / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / symbiont entry into host cell / external side of plasma membrane / negative regulation of gene expression / viral envelope / calcium ion binding / positive regulation of gene expression / virion attachment to host cell / Golgi apparatus / cell surface / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Albertini, A.A. / Belot, L. / Legrand, P. / Gaudin, Y. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein. Authors: Nikolic, J. / Belot, L. / Raux, H. / Legrand, P. / Gaudin, Y. / A Albertini, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oyl.cif.gz | 198.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oyl.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oyl_validation.pdf.gz | 474.7 KB | Display | wwPDB validaton report |
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Full document | 5oyl_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 5oyl_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 5oyl_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oyl ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oyl | HTTPS FTP |
-Related structure data
Related structure data | 5oy9C 5i2sS 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 5 molecules AD
#1: Protein | Mass: 46097.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP References: UniProt: B7UCZ5 |
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#2: Protein/peptide | Mass: 4853.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Escherichia coli (E. coli) / References: UniProt: P01130 |
#3: Sugar |
-Non-polymers , 3 types, 158 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 4.44 Å3/Da / Density % sol: 72.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 29% PEG 3000, 100 mM Tris-HCl pH 8.5, 200 mM LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→49.68 Å / Num. obs: 39498 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.061 / Rrim(I) all: 0.203 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2829 / CC1/2: 0.494 / Rpim(I) all: 1.741 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I2S Resolution: 2.25→29.979 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||
Displacement parameters | Biso max: 258.33 Å2 / Biso mean: 59.5437 Å2 / Biso min: 21.93 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→29.979 Å
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