+Open data
-Basic information
Entry | Database: PDB / ID: 3c0c | ||||||
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Title | X-ray Crystal Structure of the Rat Endophilin A2 SH3 Domain | ||||||
Components | Endophilin-A2 | ||||||
Keywords | ENDOCYTOSIS / SH3 / voltage-gated calcium channel / Endosome / Lipid-binding / Membrane / Phosphoprotein / Proto-oncogene / SH3 domain | ||||||
Function / homology | Function and homology information Negative regulation of MET activity / EGFR downregulation / synaptic vesicle uncoating / beta-1 adrenergic receptor binding / : / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / podosome / regulation of synaptic vesicle endocytosis ...Negative regulation of MET activity / EGFR downregulation / synaptic vesicle uncoating / beta-1 adrenergic receptor binding / : / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / podosome / regulation of synaptic vesicle endocytosis / modulation of excitatory postsynaptic potential / postsynaptic density, intracellular component / phosphatase binding / hippocampal mossy fiber to CA3 synapse / cell projection / SH3 domain binding / presynapse / GTPase binding / early endosome membrane / transmembrane transporter binding / glutamatergic synapse / lipid binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Loll, P.J. / Swain, E. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the SH3 domain of rat endophilin A2 Authors: Loll, P.J. / Swain, E. / Chen, Y. / Turner, B.T. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c0c.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c0c.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/3c0c ftp://data.pdbj.org/pub/pdb/validation_reports/c0/3c0c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8299.041 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sh3gl1, Sh3p8 / Plasmid: GST-parallel / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O35964 |
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#2: 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: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop vapor diffusion / pH: 6.5 Details: 1.9 M magnesium sulfate, 0.1 M MES, pH 6.5, hanging drop vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9000, 0.9795, 0.9798 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.41→34.89 Å / Num. obs: 13188 / % possible obs: 75.2 % / Redundancy: 9.04 % / Rmerge(I) obs: 0.081 / Χ2: 0.92 / Net I/σ(I): 11 / Scaling rejects: 1668 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.207 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.328 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.721 Å / Origin y: 13.262 Å / Origin z: 4.591 Å
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