[English] 日本語
Yorodumi- 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 | ||||||
Components |
| ||||||
Keywords | PROTEIN BINDING / Arc / capsid homology / GKAP | ||||||
Function / homology | Function and homology information postsynaptic endosome / 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 ...postsynaptic endosome / 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 / 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 / dendritic spine / postsynaptic density / molecular adaptor activity / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / protein-containing complex binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hallin, E.I. / Bramham, C.R. / Kursula, P. | ||||||
Funding support | Norway, 1items
| ||||||
Citation | Journal: Biochem Biophys Rep / Year: 2021 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tnq.cif.gz | 168.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tnq.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/6tnq ftp://data.pdbj.org/pub/pdb/validation_reports/tn/6tnq | HTTPS FTP |
---|
-Related structure data
Related structure data | 6tn7C 6tnoC 6tq0C 4x3hS C: citing same article (ref.) 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.) Homo sapiens (human) / Gene: ARC, KIAA0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LC44 #2: Protein/peptide | Mass: 981.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14490*PLUS #3: Chemical | ChemComp-ACE / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å |
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: MOLECULAR REPLACEMENT 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 |
|