[English] 日本語
![](img/lk-miru.gif)
- PDB-6tnq: Crystal structure of the human Arc N-lobe bound to repeat 4 from GKAP -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6tnq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human Arc N-lobe bound to repeat 4 from GKAP | ||||||
![]() |
| ||||||
![]() | PROTEIN BINDING / Arc / capsid homology / GKAP | ||||||
Function / homology | ![]() postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / postsynaptic specialization / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis ...postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / postsynaptic specialization / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis / response to morphine / regulation of postsynaptic neurotransmitter receptor internalization / Neurexins and neuroligins / regulation of long-term synaptic potentiation / anterior/posterior pattern specification / regulation of long-term synaptic depression / regulation of neuronal synaptic plasticity / mRNA transport / long-term memory / cytoskeleton organization / acrosomal vesicle / learning / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / endocytosis / extracellular vesicle / cell migration / actin cytoskeleton / cell cortex / early endosome membrane / chemical synaptic transmission / response to ethanol / dendritic spine / molecular adaptor activity / postsynaptic density / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / protein-containing complex binding / structural molecule activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hallin, E.I. / Bramham, C.R. / Kursula, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural properties and peptide ligand binding of the capsid homology domains of human Arc. Authors: Hallin, E.I. / Bramham, C.R. / Kursula, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 168.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 475 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tn7C ![]() 6tnoC ![]() 6tq0C ![]() 4x3hS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 8863.826 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 981.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-ACE / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.2 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. obs: 46481 / % possible obs: 89.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.032 / Rsym value: 0.027 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.3→1.34 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1546 / CC1/2: 0.963 / Rrim(I) all: 0.179 / Rsym value: 0.138 / % possible all: 40.4 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4x3h Resolution: 1.3→100 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.56 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→100 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|