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Open data
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Basic information
Entry | Database: PDB / ID: 6fkm | |||||||||
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Title | Drosophila Plexin A in complex with Semaphorin 1b | |||||||||
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![]() | SIGNALING PROTEIN / semaphorin / plexin / sema domain / cell-cell signaling | |||||||||
Function / homology | ![]() RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / guanylate cyclase activator activity / embryonic development via the syncytial blastoderm ...RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / guanylate cyclase activator activity / embryonic development via the syncytial blastoderm / semaphorin receptor binding / sensory neuron axon guidance / negative regulation of axon extension involved in axon guidance / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of guanylate cyclase activity / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex / axon midline choice point recognition / neural crest cell migration / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / semaphorin-plexin signaling pathway / regulation of cell migration / 14-3-3 protein binding / GTPase activator activity / axon guidance / heparin binding / regulation of cell shape / Ras protein signal transduction / positive regulation of cell migration / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rozbesky, D. / Harlos, K. / Jones, E.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of semaphorin-plexin cis interaction. Authors: Rozbesky, D. / Verhagen, M.G. / Karia, D. / Nagy, G.N. / Alvarez, L. / Robinson, R.A. / Harlos, K. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.2 KB | Display | ![]() |
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PDB format | ![]() | 346.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fknC ![]() 3okyS ![]() 6fkkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 78699.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PlexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA, PlexA1, CG11081, Dmel_CG11081 Variant: isoform A / Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: ![]() | ||
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#2: Protein | Mass: 64212.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446 Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: ![]() | ||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M HEPES (pH 7.0) and 8% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→76.864 Å / Num. obs: 31584 / % possible obs: 93.78 % / Redundancy: 4.6 % / Biso Wilson estimate: 69.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.174 / Net I/σ(I): 8.86 |
Reflection shell | Resolution: 2.96→3.07 Å / Rmerge(I) obs: 0.634 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OKY, 6FKK Resolution: 2.96→76.864 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→76.864 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: 43.7609 Å / Origin y: -9.6535 Å / Origin z: -38.6108 Å
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Refinement TLS group | Selection details: all |