[English] 日本語
![](img/lk-miru.gif)
- PDB-6qji: Crystal Structure of the third PDZ domain of PSD-95 protein: spac... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6qji | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 | |||||||||
![]() | Disks large homolog 4 | |||||||||
![]() | SIGNALING PROTEIN / pdz domain | |||||||||
Function / homology | ![]() LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / embryo development / receptor localization to synapse ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / embryo development / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / Synaptic adhesion-like molecules / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / juxtaparanode region of axon / negative regulation of receptor internalization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / Neurexins and neuroligins / regulation of NMDA receptor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Signaling by ERBB4 / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / positive regulation of excitatory postsynaptic potential / social behavior / AMPA glutamate receptor complex / Long-term potentiation / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / positive regulation of synaptic transmission / extrinsic component of cytoplasmic side of plasma membrane / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / learning / synaptic membrane / PDZ domain binding / adherens junction / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / kinase binding / cell-cell adhesion / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Camara-Artigas, A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95. Authors: Camara-Artigas, A. / Murciano-Calles, J. / Martinez, J.C. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 317.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 267.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 479.3 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qjdC ![]() 6qjfC ![]() 6qjgC ![]() 6qjjC ![]() 6qjkC ![]() 6qjlC ![]() 6qjnC ![]() 3k82S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
2 | ![]()
| |||||||||||||||
3 | ![]()
| |||||||||||||||
4 | ![]()
| |||||||||||||||
5 | ![]()
| |||||||||||||||
6 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 10660.919 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M AMMONIUM SULPHATE, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→19.97 Å / Num. obs: 80715 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 16.6 / Num. measured all: 618089 / Scaling rejects: 133 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3K82 Resolution: 1.5→19.972 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 26.11 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.42 Å2 / Biso mean: 23.5923 Å2 / Biso min: 6.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.972 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
|