+Open data
-Basic information
Entry | Database: PDB / ID: 5lo8 | ||||||
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Title | The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 | ||||||
Components | Rabphilin-3A | ||||||
Keywords | PROTEIN TRANSPORT / vesicle fusion / PIP2 / C2 domain | ||||||
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: 2.5 Å | ||||||
Authors | Ferrer-Orta, C. / Verdaguer, N. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural characterization of the Rabphilin-3A-SNAP25 interaction. Authors: Ferrer-Orta, C. / Perez-Sanchez, M.D. / Coronado-Parra, T. / Silva, C. / Lopez-Martinez, D. / Baltanas-Copado, J. / Gomez-Fernandez, J.C. / Corbalan-Garcia, S. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lo8.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lo8.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lo8_validation.pdf.gz | 960.9 KB | Display | wwPDB validaton report |
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Full document | 5lo8_full_validation.pdf.gz | 967.7 KB | Display | |
Data in XML | 5lo8_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5lo8_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5lo8 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5lo8 | HTTPS FTP |
-Related structure data
Related structure data | 5lobC 5lowC 2cm5S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18579.307 Da / Num. of mol.: 2 / Fragment: C2B domain, UNP Residues 536-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P47709 |
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-Non-polymers , 5 types, 43 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: 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: 2.31 Å3/Da / Density % sol: 20.14 % / Description: thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→65.422 Å / Num. obs: 11782 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.3 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CM5 Resolution: 2.5→65.422 Å / Cross valid method: FREE R-VALUE / σ(F): 98 / Phase error: 37.65 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→65.422 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 118.9748 Å / Origin y: 20.3093 Å / Origin z: -49.0305 Å
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Refinement TLS group | Selection details: all |