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- PDB-6tq0: Crystal structure of the human Arc N-lobe bound to repeat peptide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tq0 | ||||||
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Title | Crystal structure of the human Arc N-lobe bound to repeat peptide 5 from GKAP | ||||||
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![]() | 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.2 KB | Display | ![]() |
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PDB format | ![]() | 196.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 533 KB | Display | ![]() |
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Full document | ![]() | 540.1 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tn7C ![]() 6tnoSC ![]() 6tnqC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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7 | ![]()
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8 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8863.826 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 999.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % |
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Crystal grow | Temperature: 277 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 |
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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: 1.95→100 Å / Num. obs: 41702 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 53.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Rsym value: 0.045 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3069 / CC1/2: 0.4 / Rrim(I) all: 2.073 / Rsym value: 1.786 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6tno Resolution: 1.95→100 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 65.89 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→100 Å
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Refine LS restraints |
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