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- PDB-8blj: Crystal structure of the ligand-binding domain (LBD) of human iGl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8blj | |||||||||
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Title | Crystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1), apo state | |||||||||
![]() | Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1 | |||||||||
![]() | MEMBRANE PROTEIN / ion channel / ligand binding domain / glutamate receptor / apo state | |||||||||
Function / homology | ![]() glutamate receptor activity / glutamate receptor signaling pathway / regulation of postsynapse organization / social behavior / GABA-ergic synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / glutamatergic synapse ...glutamate receptor activity / glutamate receptor signaling pathway / regulation of postsynapse organization / social behavior / GABA-ergic synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 763.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bn2C ![]() 8bn5C ![]() 2v3tS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein / Sugars , 2 types, 12 molecules ABCDEF![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 31347.420 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 307 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 17% (w/v) polyethylene glycol (PEG) 20000, 100 mM Tris HCl, 100 mM MgCl2 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→98.31 Å / Num. obs: 56271 / % possible obs: 91.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.11 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.18→2.39 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1959 / CC1/2: 0.641 / Rpim(I) all: 0.477 / % possible all: 61.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V3T Resolution: 2.18→62.59 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9354 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→62.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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