[English] 日本語
Yorodumi- PDB-1q3p: Crystal structure of the Shank PDZ-ligand complex reveals a class... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q3p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization | ||||||
Components |
| ||||||
Keywords | PEPTIDE BINDING PROTEIN / shank / PDZ / GKAP | ||||||
Function / homology | Function and homology information somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / adult behavior / positive regulation of dendritic spine development / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / long-term memory / G protein-coupled receptor binding / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / SH3 domain binding / signaling receptor complex adaptor activity / scaffold protein binding / protein-containing complex assembly / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Im, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization Authors: Im, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q3p.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q3p.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1q3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3p_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1q3p_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 1q3p_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1q3p_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3p ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3p | HTTPS FTP |
-Related structure data
Related structure data | 1q3oSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12073.959 Da / Num. of mol.: 2 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: shank1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WV48 #2: Protein/peptide | Mass: 717.791 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: EAQTRL sequence is the C-terminal hexapeptide of GKAP protein in rattus norvegicus References: GenBank: 19923689 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Park, S.H., (2002) Acta Cryst., D58, 1353. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. all: 64296 / Num. obs: 61853 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 50.9 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.258 / % possible all: 96.5 |
Reflection shell | *PLUS % possible obs: 95.6 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q3O Resolution: 2.25→29.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 840523.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.5189 Å2 / ksol: 0.359095 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→29.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|