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Yorodumi- PDB-8bn2: Crystal structure of the ligand-binding domain (LBD) of human iGl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bn2 | |||||||||
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Title | Crystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1) in complex with D-Serine | |||||||||
Components | Glutamate receptor ionotropic, delta-1 | |||||||||
Keywords | MEMBRANE PROTEIN / ion channel / ligand binding domain / glutamate receptor / D-Serine | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Heroven, C. / Malinauskas, T. / Aricescu, A.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Science / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bn2.cif.gz | 390.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bn2.ent.gz | 267.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bn2_validation.pdf.gz | 824 KB | Display | wwPDB validaton report |
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Full document | 8bn2_full_validation.pdf.gz | 826.5 KB | Display | |
Data in XML | 8bn2_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 8bn2_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/8bn2 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/8bn2 | HTTPS FTP |
-Related structure data
Related structure data | 8bljC 8bn5C 2v3uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 31347.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRID1, KIAA1220 / Plasmid: pHR-CMV-TetO2 / Details (production host): transient transfection / Cell (production host): epithelial-like / Cell line (production host): HEK293S GnTI-/- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: Q9ULK0 #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 288 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #5: Chemical | ChemComp-DSN / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (w/v) PEG 4000, 100 mM Tris pH 7.5, 200 mM CaCl2 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 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: 1.63→87.95 Å / Num. obs: 59381 / % possible obs: 94.2 % / Redundancy: 7 % / Biso Wilson estimate: 32.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.63→1.72 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2970 / CC1/2: 0.529 / Rpim(I) all: 0.496 / % possible all: 51.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V3U Resolution: 1.63→37.45 Å / SU ML: 0.2058 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.589 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: 48.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→37.45 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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