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Yorodumi- PDB-4uwx: Structure of liprin-alpha3 in complex with mDia1 Diaphanous- inhi... -
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-Basic information
Entry | Database: PDB / ID: 4uwx | ||||||
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Title | Structure of liprin-alpha3 in complex with mDia1 Diaphanous- inhibitory domain | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PEPTIDE-BINDING PROTEIN / ACTIN POLYMERISATION / RHOGNBPS / SYNAPE MATURATION / CELL MOTILITY / FH1 / FH2 DOMAIN / ACTIN-NUCLEATION FACTOR - DIAPHANOUS-RELATED FORMIN | ||||||
Function / homology | Function and homology information epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / RHOF GTPase cycle / RHOB GTPase cycle ...epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / Receptor-type tyrosine-protein phosphatases / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction / synaptic vesicle docking / RHO GTPases Activate Formins / protein localization to microtubule / profilin binding / cellular response to histamine / presynaptic active zone cytoplasmic component / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / axon midline choice point recognition / regulation of cytoskeleton organization / presynaptic active zone / synaptic vesicle exocytosis / brush border / synaptic vesicle endocytosis / ephrin receptor signaling pathway / cytoskeleton organization / actin filament polymerization / Neutrophil degranulation / acrosomal vesicle / actin filament / sensory perception of sound / synapse organization / brain development / protein localization / small GTPase binding / mitotic spindle / ruffle membrane / neuron projection development / presynapse / gene expression / actin binding / regulation of cell shape / actin cytoskeleton organization / transmembrane transporter binding / neuron projection / positive regulation of cell migration / centrosome / glutamatergic synapse / synapse / nucleus / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Brenig, J. / de Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. ...Brenig, J. / de Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. / Neundorf, I. / Lammers, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural and Biochemical Basis for the Inhibitory Effect of Liprin-Alpha3 on Mouse Diaphanous 1 (Mdia1) Function. Authors: Brenig, J. / De Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. / Neundorf, I. / Lammers, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uwx.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwx.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwx ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwx | HTTPS FTP |
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-Related structure data
Related structure data | 1z2cS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27199.328 Da / Num. of mol.: 2 / Fragment: DIAPHANOUS-INHIBITORY DOMAIN, RESIDUES 135-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O08808 #2: Protein/peptide | Mass: 2227.567 Da / Num. of mol.: 2 / Fragment: COILED-COIL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60469 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2 M NACL, 0.1 M TRIS/HCL PH 8.0, 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2013 / Details: MIRRORS TOROIDAL FOCUSSING |
Radiation | Monochromator: BARTELS SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→105.37 Å / Num. obs: 75030 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.13 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.37 |
Reflection shell | Resolution: 1.65→1.66 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.33 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z2C Resolution: 1.65→32.317 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.093 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→32.317 Å
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