+Open data
-Basic information
Entry | Database: PDB / ID: 4q4f | |||||||||
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Title | Crystal structure of LIMP-2 (space group C2) | |||||||||
Components | Lysosome membrane protein 2 | |||||||||
Keywords | CELL ADHESION / Lysosomal targeting / beta-glucocerebrosidase / CI-MPR / ER / endosome / lysosome | |||||||||
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 / protein targeting to lysosome / scavenger receptor activity / 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 / protein targeting to lysosome / scavenger receptor activity / phosphatidylcholine binding / cargo receptor activity / cholesterol binding / phosphatidylserine binding / lysosomal lumen / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / sensory perception of sound / transmembrane signaling receptor activity / positive regulation of neuron projection development / Cargo recognition for clathrin-mediated endocytosis / endocytic vesicle membrane / Clathrin-mediated endocytosis / virus receptor activity / late endosome membrane / protein-folding chaperone binding / endosome membrane / Golgi membrane / lysosomal 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: 2.8 Å | |||||||||
Authors | Zhao, Y. / Ren, J. / Padilla-Parra, S. / Fry, L.E. / Stuart, D.I. | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Lysosome sorting of beta-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor. Authors: Zhao, Y. / Ren, J. / Padilla-Parra, S. / Fry, E.E. / Stuart, D.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q4f.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q4f.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 4q4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q4f_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 4q4f_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 4q4f_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4q4f_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4f ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4f | HTTPS FTP |
-Related structure data
Related structure data | 4q4bSC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Non-polymers , 2 types, 2 molecules A
#1: Protein | Mass: 47727.750 Da / Num. of mol.: 1 / Fragment: Human Limp-2 luminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCARB2, CD36L2, LIMP2, LIMPII / Plasmid: pNeoSec / Cell line (production host): HEK 293S GNTI- / Production host: homo sapiens (human) / References: UniProt: Q14108 |
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#8: Chemical | ChemComp-CL / |
-Sugars , 6 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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 #4: 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 | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 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 | 6-O-phosphono-beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)- ...6-O-phosphono-beta-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 #7: Sugar | |
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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: 3.33 Å3/Da / Density % sol: 63.04 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30 %w/v Polyethylene Glycol 8000, 0.2 M Ammonium Sulphate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 15244 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.8 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4Q4B Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.885 / SU B: 46.978 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R: 2.797 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 71.184 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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