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- PDB-5kc9: Crystal structure of the amino-terminal domain (ATD) of iGluR Del... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kc9 | ||||||
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Title | Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-1 (GluD1) | ||||||
![]() | Glutamate receptor ionotropic, delta-1 | ||||||
![]() | SIGNALING PROTEIN / ionotropic glutamate receptor (iGluR) / neurotransmission | ||||||
Function / homology | ![]() : / glutamate receptor activity / social behavior / ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / modulation of chemical synaptic transmission / signaling receptor activity / postsynaptic membrane ...: / glutamate receptor activity / social behavior / ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / modulation of chemical synaptic transmission / signaling receptor activity / postsynaptic membrane / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elegheert, J. / Clay, J.E. / Siebold, C. / Aricescu, A.R. | ||||||
![]() | ![]() Title: Structural basis for integration of GluD receptors within synaptic organizer complexes. Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / ...Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / Greger, I.H. / Nakagawa, T. / Yuzaki, M. / Aricescu, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.4 KB | Display | ![]() |
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PDB format | ![]() | 198.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.9 KB | Display | ![]() |
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Full document | ![]() | 532.1 KB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kc5C ![]() 5kc6C ![]() 5kc7C ![]() 5kc8SC ![]() 5kcaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
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Components
-Protein / Sugars , 2 types, 6 molecules ABC![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 48395.785 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Sugar | |
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-Non-polymers , 5 types, 225 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES (2-ethanesulfonic acid)/imidazole pH 6.5, 10% (w/v) polyethylene glycol 8000, 20% (w/v) ethylene glycol, 0.02 M 1,6-hexanediol, 0.02 M (RS)-1,2-propanediol, 0.02 M 1-butanol, 0.02 ...Details: 0.1 M MES (2-ethanesulfonic acid)/imidazole pH 6.5, 10% (w/v) polyethylene glycol 8000, 20% (w/v) ethylene glycol, 0.02 M 1,6-hexanediol, 0.02 M (RS)-1,2-propanediol, 0.02 M 1-butanol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol and 0.02 M 1,3-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→59.22 Å / Num. obs: 65080 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 57.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.222 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KC8 Resolution: 2.3→59.22 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
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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: 77.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→59.22 Å
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Refine LS restraints |
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LS refinement shell |
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