+Open data
-Basic information
Entry | Database: PDB / ID: 8qf4 | ||||||
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Title | Complex between N-lobe of Arc and nanobody H11 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / nanobody | ||||||
Function / homology | Function and homology information postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / 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 ...postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / 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 / 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 / dendritic spine / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Vicugna pacos (alpaca) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Godoy Munoz, J.M. / Kursula, P. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Complex between Arc N-lobe and nanobody H11 Authors: Godoy Munoz, J.M. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qf4.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qf4.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/8qf4 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/8qf4 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 14078.622 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) | ||||
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#2: Protein | Mass: 8863.826 Da / Num. of mol.: 1 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 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M potassium phosphate citrate pH 4.2, 0.2 M NaCl and 20% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.83 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→50 Å / Num. obs: 168367 / % possible obs: 94.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.02→1.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 14404 / CC1/2: 0.233 / Rrim(I) all: 2.047 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→35.16 Å / SU ML: 0.1388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2606 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→35.16 Å
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Refine LS restraints |
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LS refinement shell |
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