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Yorodumi- PDB-5lob: Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 s... -
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-Basic information
Entry | Database: PDB / ID: 5lob | ||||||
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Title | Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) | ||||||
Components |
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Keywords | EXOCYTOSIS / membrane fusion / SNARE complex / PIP2 / C2 domain | ||||||
Function / homology | Function and homology information selenium binding / BLOC-1 complex / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / synaptic vesicle fusion to presynaptic active zone membrane ...selenium binding / BLOC-1 complex / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / synaptic vesicle fusion to presynaptic active zone membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / ribbon synapse / regulation of establishment of protein localization / calcium ion-regulated exocytosis of neurotransmitter / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / SNARE complex / SNAP receptor activity / positive regulation of hormone secretion / neurotransmitter secretion / inositol 1,4,5 trisphosphate binding / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / extrinsic component of membrane / myosin binding / exocytosis / phosphate ion binding / voltage-gated potassium channel activity / synaptic vesicle exocytosis / associative learning / long-term memory / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / somatodendritic compartment / phosphatidylinositol-4,5-bisphosphate binding / photoreceptor inner segment / axonogenesis / SNARE binding / secretory granule / filopodium / locomotory behavior / long-term synaptic potentiation / intracellular protein transport / neuromuscular junction / neuron differentiation / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / phospholipid binding / synaptic vesicle membrane / small GTPase binding / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / presynapse / lamellipodium / presynaptic membrane / cell cortex / growth cone / postsynapse / postsynaptic membrane / transmembrane transporter binding / dendritic spine / cytoskeleton / endosome / neuron projection / protein domain specific binding / axon / neuronal cell body / glutamatergic synapse / lipid binding / synapse / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / zinc ion binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 | 5lob.cif.gz | 311.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lob.ent.gz | 251.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lob_validation.pdf.gz | 518 KB | Display | wwPDB validaton report |
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Full document | 5lob_full_validation.pdf.gz | 525.4 KB | Display | |
Data in XML | 5lob_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5lob_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5lob ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5lob | HTTPS FTP |
-Related structure data
Related structure data | 5lo8C 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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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 18579.307 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Details (production host): Kanamicine resistant / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P47709 |
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-Synaptosomal-associated protein ... , 2 types, 4 molecules DFEG
#2: Protein | Mass: 11266.603 Da / Num. of mol.: 2 / Fragment: N-terminal helix Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60881 #3: Protein | Mass: 10414.731 Da / Num. of mol.: 2 / Fragment: C-terminal helix Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60881 |
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-Non-polymers , 3 types, 25 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / |
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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: 2.9 Å3/Da / Density % sol: 54.7 % / Description: thin plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5 |
-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 PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→48.42 Å / Num. obs: 12936 / % possible obs: 79.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / % possible all: 81.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CM5 Resolution: 3.3→42.527 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.58 / Stereochemistry target values: ML
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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: 3.3→42.527 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: -49.1327 Å / Origin y: -17.4485 Å / Origin z: 1.3082 Å
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Refinement TLS group | Selection details: all |