+Open data
-Basic information
Entry | Database: PDB / ID: 4ns0 | ||||||
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Title | The C2A domain of Rabphilin 3A in complex with PI(4,5)P2 | ||||||
Components | Rabphilin-3A | ||||||
Keywords | PROTEIN TRANSPORT / C2 domain / Calcium binding / phospholipid binding / RABPHILIN-3A / C2A / SYNAPTIC EXOCYTOSIS METAL-BINDING / C-2 domain fold / EXOPHILIN-1 | ||||||
Function / homology | Function and homology information selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming ...selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming / extrinsic component of membrane / exocytosis / phosphate ion binding / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / synaptic vesicle membrane / small GTPase binding / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Guillen, J. / Ferrer-Orta, C. / Buxaderas, M. / Perez-sanchez, D. / Guerrero-Valero, M. / Luengo-Gil, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Verdaguer, N. / Corbalan-Garcia, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1. Authors: Guillen, J. / Ferrer-Orta, C. / Buxaderas, M. / Perez-Sanchez, D. / Guerrero-Valero, M. / Luengo-Gil, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Verdaguer, N. / Corbalan-Garcia, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ns0.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ns0.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ns0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ns0_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 4ns0_full_validation.pdf.gz | 765.6 KB | Display | |
Data in XML | 4ns0_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4ns0_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4ns0 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4ns0 | HTTPS FTP |
-Related structure data
Related structure data | 4lt7C 4np9C 2chdS 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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Unit cell |
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-Components
#1: Protein | Mass: 15305.478 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP RESIDUES 378-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Production host: Escherichia coli (E. coli) / References: UniProt: P47709 |
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#2: Chemical | ChemComp-PIO / [( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25mM Hepes, 20mM Ammonuim Sulphate, 25% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.36 Å / Num. obs: 12421 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.131 / Rsym value: 0.061 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.78→1.89 Å / Rmerge(I) obs: 0.72 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CHD Resolution: 1.8→44.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.744 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / 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: 24.048 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.36 Å
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