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- PDB-5v6e: Crystal structure of Myosin VI in complex with GH2 domain of GIPC1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v6e | |||||||||
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Title | Crystal structure of Myosin VI in complex with GH2 domain of GIPC1 | |||||||||
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![]() | PROTEIN BINDING / helical bundle | |||||||||
Function / homology | ![]() FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / Trafficking of AMPA receptors / cellular response to electrical stimulus ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / Trafficking of AMPA receptors / cellular response to electrical stimulus / positive regulation of melanin biosynthetic process / postsynaptic neurotransmitter receptor internalization / actin filament-based movement / postsynaptic actin cytoskeleton / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / vesicle membrane / glutamate secretion / cellular response to interleukin-7 / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / dendrite development / positive regulation of cytokinesis / brush border / microvillus / inner ear development / endocytic vesicle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / endothelial cell migration / protein targeting / clathrin-coated pit / ruffle / synapse assembly / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / dendritic shaft / filopodium / locomotory behavior / PDZ domain binding / actin filament organization / sensory perception of sound / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / regulation of protein stability / protein localization / ruffle membrane / endocytosis / actin filament binding / protein transport / actin cytoskeleton / synaptic vesicle / presynapse / apical part of cell / actin binding / cell cortex / cytoplasmic vesicle / postsynapse / chemical synaptic transmission / dendritic spine / postsynaptic density / calmodulin binding / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shang, G. / Zhang, X. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.3 KB | Display | ![]() |
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PDB format | ![]() | 207.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.7 KB | Display | ![]() |
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Full document | ![]() | 494.9 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v6bC ![]() 5v6hSC ![]() 5v6rC ![]() 5v6tC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8962.971 Da / Num. of mol.: 5 / Fragment: UNP residues 258-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 5786.563 Da / Num. of mol.: 5 / Fragment: UNP residues 1055-1099 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.49 Å3/Da / Density % sol: 77.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.0 and 2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 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: 3.5→50 Å / Num. obs: 20339 / % possible obs: 97 % / Redundancy: 6.1 % / Rpim(I) all: 0.074 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 6 % / Rpim(I) all: 0.493 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5V6H Resolution: 3.506→47.082 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 22.45 / 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: 3.506→47.082 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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