[English] 日本語
![](img/lk-miru.gif)
- PDB-4jra: CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jra | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C | ||||||
![]() |
| ||||||
![]() | HYDROLASE / Beta-helix / Vesicles / lumen / toxin | ||||||
Function / homology | ![]() Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / host cell junction / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport ...Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / host cell junction / Toxicity of botulinum toxin type A (botA) / dopaminergic synapse / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / neurotransmitter transport / host cell cytosol / regulation of synaptic vesicle exocytosis / transmembrane transporter activity / protein transmembrane transporter activity / metalloendopeptidase activity / synaptic vesicle membrane / synaptic vesicle / toxin activity / chemical synaptic transmission / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Benoit, R.M. / Frey, D. / Wieser, M.M. / Jaussi, R. / Schertler, G.F.X. / Capitani, G. / Kammerer, R.A. | ||||||
![]() | ![]() Title: Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A. Authors: Benoit, R.M. / Frey, D. / Hilbert, M. / Kevenaar, J.T. / Wieser, M.M. / Stirnimann, C.U. / McMillan, D. / Ceska, T. / Lebon, F. / Jaussi, R. / Steinmetz, M.O. / Schertler, G.F. / Hoogenraad, ...Authors: Benoit, R.M. / Frey, D. / Hilbert, M. / Kevenaar, J.T. / Wieser, M.M. / Stirnimann, C.U. / McMillan, D. / Ceska, T. / Lebon, F. / Jaussi, R. / Steinmetz, M.O. / Schertler, G.F. / Hoogenraad, C.C. / Capitani, G. / Kammerer, R.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 394.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 324.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3fuoS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 51724.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin #2: Protein | Mass: 15984.894 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2012 |
Radiation | Monochromator: FIXED EXIT DOUBLE, CHANNEL DCM MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 67843 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3FUO Resolution: 2.3→19.933 Å / Isotropic thermal model: isotropic / σ(F): 1.36 / Phase error: 27.58 / Stereochemistry target values: TWIN_LSQ_F / Details: twin operator -h, -k, l
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.933 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|