+Open data
-Basic information
Entry | Database: PDB / ID: 3q84 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human PACSIN 1 F-BAR domain | ||||||
Components | Protein kinase C and casein kinase substrate in neurons protein 1 | ||||||
Keywords | ENDOCYTOSIS / Alpha helix / Cytoplasmic vesicle | ||||||
Function / homology | Function and homology information presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / negative regulation of endocytosis / protein localization to membrane / positive regulation of dendrite development / synaptic vesicle endocytosis / regulation of endocytosis / axon terminus ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / negative regulation of endocytosis / protein localization to membrane / positive regulation of dendrite development / synaptic vesicle endocytosis / regulation of endocytosis / axon terminus / cytoskeleton organization / cytoskeletal protein binding / neuron projection morphogenesis / actin filament organization / protein localization to plasma membrane / phospholipid binding / cytoplasmic vesicle membrane / ruffle membrane / Clathrin-mediated endocytosis / endosome / synapse / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Bai, X. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human PACSIN 1 F-BAR domain Authors: Bai, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q84.cif.gz | 343.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q84.ent.gz | 294.1 KB | Display | PDB format |
PDBx/mmJSON format | 3q84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/3q84 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/3q84 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35485.594 Da / Num. of mol.: 6 / Fragment: hPACSIN 1 (UNP RESIDUES 14-308) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BY11 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200mM NH4H2PO4, 100mM HEPES pH 7.5, 16% PEG 3350 (w/v), 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.06 Å / Num. all: 74726 / Num. obs: 63354 / % possible obs: 96.203 % |
Reflection shell | Resolution: 2.83→2.91 Å / % possible all: 96.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.8→29.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.511 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.693 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
|