+Open data
-Basic information
Entry | Database: PDB / ID: 5v6t | |||||||||
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Title | The Plexin D1 intracellular region in complex with GIPC1 | |||||||||
Components |
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Keywords | PROTEIN BINDING | |||||||||
Function / homology | Function and homology information FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / Other semaphorin interactions / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / cardiac septum development / synaptic target recognition / positive regulation of melanin biosynthetic process / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / Other semaphorin interactions / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / cardiac septum development / synaptic target recognition / positive regulation of melanin biosynthetic process / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / vesicle membrane / coronary vasculature development / negative regulation of cell adhesion / glutamate secretion / semaphorin receptor complex / cellular response to interleukin-7 / aorta development / branching involved in blood vessel morphogenesis / positive regulation of axonogenesis / myosin binding / regulation of GTPase activity / outflow tract morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / lamellipodium membrane / brush border / semaphorin-plexin signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / endocytic vesicle / endothelial cell migration / protein targeting / regulation of angiogenesis / regulation of cell migration / synapse assembly / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / dendritic shaft / kidney development / PDZ domain binding / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / regulation of protein stability / synaptic vesicle / presynapse / positive regulation of protein binding / lamellipodium / actin binding / cell cortex / cell body / regulation of cell shape / postsynapse / chemical synaptic transmission / angiogenesis / negative regulation of neuron apoptotic process / dendritic spine / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / signaling receptor binding / glutamatergic synapse / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 Å | |||||||||
Authors | Shang, G. / Zhang, X. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2017 Title: Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex. Authors: Shang, G. / Brautigam, C.A. / Chen, R. / Lu, D. / Torres-Vazquez, J. / Zhang, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v6t.cif.gz | 290.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v6t.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 5v6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/5v6t ftp://data.pdbj.org/pub/pdb/validation_reports/v6/5v6t | HTTPS FTP |
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-Related structure data
Related structure data | 5v6bC 5v6eC 5v6hC 5v6rSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 67870.641 Da / Num. of mol.: 1 / Fragment: UNP residues 1339-1925 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UH93 | ||
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#2: Protein | Mass: 31541.020 Da / Num. of mol.: 1 / Fragment: UNP residues 52-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gipc1, Gipc, Rgs19ip1, Semcap1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0G0 | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 27629 / % possible obs: 100 % / Redundancy: 12 % / Rpim(I) all: 0.041 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.361 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V6R Resolution: 3.189→49.033 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 19.96 / 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: 3.189→49.033 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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