[English] 日本語
![](img/lk-miru.gif)
- PDB-5heb: The third PDZ domain from the synaptic protein PSD-95 in complex ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5heb | ||||||
---|---|---|---|---|---|---|---|
Title | The third PDZ domain from the synaptic protein PSD-95 in complex with a C-terminal peptide derived from CRIPT | ||||||
![]() |
| ||||||
![]() | PEPTIDE BINDING PROTEIN / PDZ / GLGF / DHR / adhesion / synapse / synaptic density / peptide-binding domain | ||||||
Function / homology | ![]() regulation of postsynaptic density protein 95 clustering / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / protein localization to microtubule / regulation of postsynaptic density assembly ...regulation of postsynaptic density protein 95 clustering / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / protein localization to microtubule / regulation of postsynaptic density assembly / structural constituent of postsynaptic density / proximal dendrite / 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 / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / dendritic branch / neuron spine / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / juxtaparanode region of axon / frizzled binding / negative regulation of receptor internalization / dendritic spine organization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / positive regulation of excitatory postsynaptic potential / social behavior / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / beta-2 adrenergic receptor binding / cytoplasmic microtubule organization / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / RNA splicing / dendritic shaft / synaptic membrane / cell periphery / PDZ domain binding / postsynaptic density membrane / spliceosomal complex / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / mRNA processing / cerebral cortex development / kinase binding / cell-cell adhesion / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / postsynapse / microtubule binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | White, K.I. / Raman, A.S. / Ranganathan, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Origins of Allostery and Evolvability in Proteins: A Case Study. Authors: Raman, A.S. / White, K.I. / Ranganathan, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hedC ![]() 5hetC ![]() 5heyC ![]() 5hf1C ![]() 5hfbC ![]() 5hfcC ![]() 5hffC ![]() 1be9S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 12738.067 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein/peptide | Mass: 1070.196 Da / Num. of mol.: 1 / Fragment: PDZ3-binding domain (UNP residues 93-101) / Source method: obtained synthetically Details: Synthesized using standard FMOC chemistry, HPCL purified, and lyophilized. Source: (synth.) ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein ...Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer. |
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40.147 Å / Num. obs: 15083 / % possible obs: 97.6 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 61.571 |
Reflection shell | Resolution: 1.65→1.703 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.478 / % possible all: 76 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1BE9 Resolution: 1.65→40.147 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 18.11 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→40.147 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|