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Yorodumi- PDB-4x9f: Crystal structure of Dscam1 isoform 6.9, N-terminal four Ig domains -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x9f | |||||||||
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Title | Crystal structure of Dscam1 isoform 6.9, N-terminal four Ig domains | |||||||||
Components | Down Syndrome Cell Adhesion Molecule isoform 6.9 | |||||||||
Keywords | CELL ADHESION / Ig fold | |||||||||
Function / homology | Function and homology information DSCAM interactions / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity ...DSCAM interactions / mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation / regulation of dendrite morphogenesis / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / phagocytosis / antigen binding / axon guidance / perikaryon / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Chen, Q. / Yu, Y. / Li, S.A. / Cheng, L. | |||||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition Authors: Li, S.A. / Cheng, L. / Yu, Y. / Chen, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x9f.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x9f.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/4x9f ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x9f | HTTPS FTP |
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-Related structure data
Related structure data | 4wvrC 4x5lC 4x83C 4x8xC 4x9bC 4x9gC 4x9hC 4x9iC 4xb7C 4xb8C 4xhqC 2v5mS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43546.188 Da / Num. of mol.: 2 / Fragment: N-terminal four Ig domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0E9K4*PLUS |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 233 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: 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: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES pH7.5, 0.2M Ammonium Sulfate, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 42006 / % possible obs: 99.7 % / Redundancy: 7.9 % / Net I/σ(I): 27.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V5M Resolution: 2.35→38.305 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.39 / 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: 2.35→38.305 Å
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Refine LS restraints |
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LS refinement shell |
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