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Yorodumi- PDB-4lt7: Crystal structure of the c2a domain of rabphilin-3a in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lt7 | ||||||
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Title | Crystal structure of the c2a domain of rabphilin-3a in complex with a calcium | ||||||
Components | Rabphilin-3A | ||||||
Keywords | PROTEIN TRANSPORT / calcium binding / C2 domain / signal transduction | ||||||
Function / homology | Function and homology information selenium binding / spontaneous neurotransmitter secretion / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / 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 / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / 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 / phosphate ion binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / small GTPase binding / synaptic vesicle membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Verdaguer, N. / Ferrer-Orta, C. / Buxaderas, M. / Corbalan-Garcia, S. / Perez-Sanchez, D. / Guerrero-Valero, M. / Luengo, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Guillen, J. | ||||||
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 | 4lt7.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lt7.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lt7_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 4lt7_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 4lt7_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 4lt7_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4lt7 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4lt7 | HTTPS FTP |
-Related structure data
Related structure data | 4np9C 4ns0C 2chdS S: Starting model for refinement C: citing same article (ref.) |
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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 1 domain residues 378-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P47709 |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 10 mM CaCl2, 150mM NaCl, 25mM HEPES ph 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 10, 2012 / Details: mirrors |
Radiation | Monochromator: osmic confocals focusing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 3660 / % possible obs: 72.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.9 / % possible all: 68.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CHD Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.97 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.447 / 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: 45.055 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.4876 Å / Origin y: 9.8121 Å / Origin z: 32.0332 Å
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Refinement TLS group |
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