+Open data
-Basic information
Entry | Database: PDB / ID: 6fkk | |||||||||
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Title | Drosophila Semaphorin 1b, extracellular domains 1-2 | |||||||||
Components | MIP07328p | |||||||||
Keywords | SIGNALING PROTEIN / semaphorin / sema domain / axon guidance cue / cell cell signaling | |||||||||
Function / homology | Function and homology information Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / semaphorin receptor binding / chemorepellent activity / negative chemotaxis / semaphorin-plexin signaling pathway ...Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / semaphorin receptor binding / chemorepellent activity / negative chemotaxis / semaphorin-plexin signaling pathway / axon guidance / positive regulation of cell migration / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | |||||||||
Authors | Rozbesky, D. / Harlos, K. / Jones, E.Y. | |||||||||
Funding support | United Kingdom, 1items
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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 | 6fkk.cif.gz | 233.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fkk.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fkk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fkk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fkk_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6fkk_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkk ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkk | HTTPS FTP |
-Related structure data
Related structure data | 6qp7C 6qp8C 6qp9C 3okyS 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: 64212.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446 Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7KK54 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
#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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→81.628 Å / Num. obs: 27778 / % possible obs: 96.74 % / Redundancy: 11.7 % / Biso Wilson estimate: 63.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.93 |
Reflection shell | Resolution: 2.78→2.88 Å / Rmerge(I) obs: 1.641 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OKY Resolution: 2.78→81.628 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→81.628 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: 48.6252 Å / Origin y: 39.8763 Å / Origin z: -6.0814 Å
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Refinement TLS group | Selection details: all |