[English] 日本語
![](img/lk-miru.gif)
- PDB-8bn5: Crystal structure of the ligand-binding domain (LBD) of human iGl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bn5 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1) in complex with GABA | |||||||||
![]() | Glutamate receptor ionotropic, delta-1 | |||||||||
![]() | MEMBRANE PROTEIN / ion channel / ligand binding domain / glutamate receptor / GABA | |||||||||
Function / homology | ![]() glutamate receptor signaling pathway / glutamate receptor activity / regulation of postsynapse organization / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / glutamatergic synapse ...glutamate receptor signaling pathway / glutamate receptor activity / regulation of postsynapse organization / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / glutamatergic synapse / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Heroven, C. / Malinauskas, T. / Aricescu, A.R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: GluD1 binds GABA and controls inhibitory plasticity. Authors: Piot, L. / Heroven, C. / Bossi, S. / Zamith, J. / Malinauskas, T. / Johnson, C. / Wennagel, D. / Stroebel, D. / Charrier, C. / Aricescu, A.R. / Mony, L. / Paoletti, P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 391.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 269.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bljC ![]() 8bn2C ![]() 2v3uS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 31347.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Sugar | ChemComp-NAG / | |
---|
-Non-polymers , 5 types, 235 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (w/v) PEG 4000, 100 mM HEPES pH 7.5, 200 mM CaCl2 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→87.71 Å / Num. obs: 37143 / % possible obs: 93.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.6 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.9→2.03 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.719 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1837 / CC1/2: 0.525 / Rpim(I) all: 0.6 / % possible all: 51.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2V3U Resolution: 1.9→44.35 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2351 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|