+Open data
-Basic information
Entry | Database: PDB / ID: 2x3w | ||||||
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Title | structure of mouse syndapin I (crystal form 2) | ||||||
Components | (PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1) x 2 | ||||||
Keywords | ENDOCYTOSIS / N-WASP / DYNAMIN / PACSIN I / TRANSFERASE | ||||||
Function / homology | Function and homology information presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of dendrite development / synaptic vesicle endocytosis ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of dendrite development / synaptic vesicle endocytosis / regulation of endocytosis / axon terminus / cytoskeleton organization / cytoskeletal protein binding / neuron projection morphogenesis / protein localization to plasma membrane / actin filament organization / postsynaptic density membrane / cytoplasmic vesicle membrane / phospholipid binding / ruffle membrane / myelin sheath / endosome / glutamatergic synapse / synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Ma, Q. / Rao, Y. / Saenger, W. / Haucke, V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Molecular Basis for SH3 Domain Regulation of F-Bar-Mediated Membrane Deformation. Authors: Rao, Y. / Ma, Q. / Vahedi-Faridi, A. / Sundborger, A. / Pechstein, A. / Puchkov, D. / Luo, L. / Shupliakov, O. / Saenger, W. / Haucke, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3w.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3w.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 2x3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3w ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3w | HTTPS FTP |
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-Related structure data
-Links
-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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Unit cell |
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-Components
#1: Protein | Mass: 39349.430 Da / Num. of mol.: 3 / Fragment: F-BAR DOMAIN, RESIDUES 1-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644 #2: Protein | | Mass: 6731.324 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 382-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644 #3: 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 5.3 Details: 2.5UL SYNDAPIN(5MG/ML IN 50MM HEPES, 50MM NACL) MIXED WITH 0.5UL 0.3M GLYCYL-GLYCYL-GLYCINE AND 2UL WELL SOLUTION 0.1M NAAC/HAC PH5.0, 3%(W/V) PEG4000., pH 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2009 Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→34.35 Å / Num. obs: 38766 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.17 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.81 |
Reflection shell | Resolution: 2.64→2.75 Å / Redundancy: 7.03 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.88 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→34.36 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 26.268 / SU ML: 0.257 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.332 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→34.36 Å
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Refine LS restraints |
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