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Yorodumi- PDB-5lfr: Crystal structure of glycosylated Myelin-associated glycoprotein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lfr | |||||||||
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Title | Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 | |||||||||
Components | Myelin-associated glycoprotein | |||||||||
Keywords | CELL ADHESION / myelin / cell adhesion molecule | |||||||||
Function / homology | Function and homology information mesaxon / Axonal growth inhibition (RHOA activation) / compact myelin / ganglioside GT1b binding / central nervous system myelination / sialic acid binding / myelin sheath adaxonal region / positive regulation of myelination / central nervous system myelin formation / negative regulation of axon extension ...mesaxon / Axonal growth inhibition (RHOA activation) / compact myelin / ganglioside GT1b binding / central nervous system myelination / sialic acid binding / myelin sheath adaxonal region / positive regulation of myelination / central nervous system myelin formation / negative regulation of axon extension / cell-cell adhesion via plasma-membrane adhesion molecules / paranode region of axon / Schmidt-Lanterman incisure / positive regulation of astrocyte differentiation / axon regeneration / transmission of nerve impulse / negative regulation of neuron differentiation / myelination / cellular response to mechanical stimulus / negative regulation of neuron projection development / myelin sheath / carbohydrate binding / negative regulation of neuron apoptotic process / cell adhesion / membrane raft / signaling receptor binding / protein kinase binding / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||
Authors | Pronker, M.F. / Janssen, B.J.C. | |||||||||
Funding support | Netherlands, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: Structural basis of myelin-associated glycoprotein adhesion and signalling. Authors: Pronker, M.F. / Lemstra, S. / Snijder, J. / Heck, A.J. / Thies-Weesie, D.M. / Pasterkamp, R.J. / Janssen, B.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lfr.cif.gz | 267.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lfr.ent.gz | 217.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/5lfr ftp://data.pdbj.org/pub/pdb/validation_reports/lf/5lfr | HTTPS FTP |
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-Related structure data
Related structure data | 5lf5C 5lfuC 5lfvC 1cs6S 1urlS 4frwS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35014.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mag / Plasmid: pUPE107.03 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / Variant (production host): GnTI-/- and EBNA1-expressing / References: UniProt: P20917 |
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-Sugars , 4 types, 9 molecules
#2: 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 | ||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: Sugar | #5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 64 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-SO4 / #8: 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: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97599 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97599 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→42.73 Å / Num. obs: 42931 / % possible obs: 96.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.12→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 0.9 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1URL, 4FRW, 1CS6 Resolution: 2.12→42.729 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→42.729 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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