+Open data
-Basic information
Entry | Database: PDB / ID: 6qp9 | |||||||||
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Title | Drosophila Semaphorin 1a, extracellular domains 1-2 | |||||||||
Components | Semaphorin-1A | |||||||||
Keywords | SIGNALING PROTEIN / axon guidance cue / developmental protein / cell signalling / semaphorin / signalling protein | |||||||||
Function / homology | Function and homology information semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / semaphorin receptor binding / synaptic target recognition / negative regulation of axon extension involved in axon guidance / chemorepellent activity / negative regulation of cell size / motor neuron axon guidance / axon midline choice point recognition ...semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / semaphorin receptor binding / synaptic target recognition / negative regulation of axon extension involved in axon guidance / chemorepellent activity / negative regulation of cell size / motor neuron axon guidance / axon midline choice point recognition / dendrite morphogenesis / negative chemotaxis / semaphorin-plexin signaling pathway / synapse assembly / axon guidance / heparin binding / membrane => GO:0016020 / positive regulation of cell migration / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Rozbesky, D. / Robinson, R.A. / Harlos, K. / Siebold, C. / Jones, E.Y. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning. Authors: Rozbesky, D. / Robinson, R.A. / Jain, V. / Renner, M. / Malinauskas, T. / Harlos, K. / Siebold, C. / Jones, E.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qp9.cif.gz | 413.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qp9.ent.gz | 342.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qp9 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qp9 | HTTPS FTP |
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-Related structure data
Related structure data | 6fkkSC 6qp7C 6qp8C 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
#1: Protein | Mass: 59945.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sema1a, Dsema-I, Sema-1a, CG18405 / Production host: Homo sapiens (human) / References: UniProt: Q24322 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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: 3.58 Å3/Da / Density % sol: 65.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M ammonium sulphate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→49.74 Å / Num. obs: 19133 / % possible obs: 96.98 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.233 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.6→3.82 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FKK Resolution: 3.6→49.738 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 135.19 / Phase error: 53.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→49.738 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 105.2393 Å / Origin y: -3.7203 Å / Origin z: -21.6492 Å
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Refinement TLS group | Selection details: all |