+Open data
-Basic information
Entry | Database: PDB / ID: 4tvz | ||||||||||||
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Title | Crystal Structure of SCARB2 in Neural Condition (pH7.5) | ||||||||||||
Components | Scavenger receptor class B member 2 | ||||||||||||
Keywords | PROTEIN BINDING / lipid binding tunnel | ||||||||||||
Function / homology | Function and homology information regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / regulation of lysosome organization / endosome to plasma membrane protein transport / scavenger receptor activity / protein targeting to lysosome / phosphatidylcholine binding / cargo receptor activity ...regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / regulation of lysosome organization / endosome to plasma membrane protein transport / scavenger receptor activity / protein targeting to lysosome / phosphatidylcholine binding / cargo receptor activity / cholesterol binding / phosphatidylserine binding / lysosomal lumen / receptor-mediated endocytosis / sensory perception of sound / clathrin-coated endocytic vesicle membrane / positive regulation of neuron projection development / transmembrane signaling receptor activity / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / late endosome membrane / virus receptor activity / protein-folding chaperone binding / endosome membrane / lysosomal membrane / Golgi membrane / focal adhesion / endoplasmic reticulum membrane / enzyme binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.006 Å | ||||||||||||
Model details | The protein was expressed in 293T cell | ||||||||||||
Authors | Dang, M.H. / Wang, X.X. / Rao, Z.H. | ||||||||||||
Funding support | China, 1items
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Citation | Journal: Protein Cell / Year: 2014 Title: Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71 Authors: Dang, M. / Wang, X. / Wang, Q. / Wang, Y. / Lin, J. / Sun, Y. / Li, X. / Zhang, L. / Lou, Z. / Wang, J. / Rao, Z. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tvz.cif.gz | 185 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tvz.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 4tvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tvz_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 4tvz_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 4tvz_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 4tvz_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/4tvz ftp://data.pdbj.org/pub/pdb/validation_reports/tv/4tvz | HTTPS FTP |
-Related structure data
Related structure data | 4tw0C 4tw2C 4f7bS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.999919, 0.003412, -0.012247), Vector: Details | biological unit is the same as asym. | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45219.070 Da / Num. of mol.: 2 / Fragment: ectodomain, UNP residue 37-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCARB2, CD36L2, LIMP2, LIMPII / Plasmid: PHL_Sec / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: Q14108 |
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-Sugars , 7 types, 16 molecules
#2: Polysaccharide | #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #7: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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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: 3.64 Å3/Da / Density % sol: 66.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 mol/L HEPES, 25%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 8, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 24297 / % possible obs: 92.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.02 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F7B Resolution: 3.006→34.883 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.89 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.56 Å2 / Biso mean: 39.8847 Å2 / Biso min: 6.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.006→34.883 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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