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Yorodumi- PDB-2jil: Crystal structure of 2nd PDZ domain of glutamate receptor interac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jil | ||||||
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Title | Crystal structure of 2nd PDZ domain of glutamate receptor interacting protein-1 (GRIP1) | ||||||
Components | GLUTAMATE RECEPTOR INTERACTING PROTEIN-1 | ||||||
Keywords | MEMBRANE PROTEIN / ENDOPLASMIC RETICULUM / POSTSYNAPTIC MEMBRANE / MEMBRANE | ||||||
Function / homology | Function and homology information vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / : / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / nuclear glucocorticoid receptor binding / dendrite development / beta-catenin binding / signaling receptor complex adaptor activity / cytoplasmic vesicle ...vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / : / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / nuclear glucocorticoid receptor binding / dendrite development / beta-catenin binding / signaling receptor complex adaptor activity / cytoplasmic vesicle / postsynaptic membrane / perikaryon / postsynaptic density / intracellular signal transduction / neuron projection / membrane raft / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Tickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 2Nd Pdz Domain of Glutamate Receptor Interacting Protein-1 (Grip1) Authors: Tickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jil.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jil.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jil ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jil | HTTPS FTP |
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-Related structure data
Related structure data | 1be9S 1mfgS 1n7eS 1n7fS 1tq3S 2he2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.08357, 0.99649, -0.00491), Vector: |
-Components
#1: Protein | Mass: 10429.821 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN 2, RESIDUES 149-239 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9Y3R0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | pH: 7.5 Details: 20% PEG3350, 0.20M POTASSIUM THIOCYANATE, 10% ETHYLENE GLYCOL, 0.1M BIS TRIS PROPANE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.31 Å / Num. obs: 26857 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 21.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F Resolution: 1.5→48.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.642 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→48.22 Å
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