+Open data
-Basic information
Entry | Database: PDB / ID: 5jp2 | ||||||
---|---|---|---|---|---|---|---|
Title | Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / FCHO Eps15 Mu homology domain Endocytosis | ||||||
Function / homology | Function and homology information Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling ...Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / clathrin-coated pit / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / postsynapse / receptor-mediated endocytosis of virus by host cell / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | McCoy, A.J. / Wrobel, A. / Owen, D.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Dev.Cell / Year: 2016 Title: Transient Fcho1/2Eps15/RAP-2 Nanoclusters Prime the AP-2 Clathrin Adaptor for Cargo Binding. Authors: Ma, L. / Umasankar, P.K. / Wrobel, A.G. / Lymar, A. / McCoy, A.J. / Holkar, S.S. / Jha, A. / Pradhan-Sundd, T. / Watkins, S.C. / Owen, D.J. / Traub, L.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jp2.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jp2.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 5jp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jp2 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jp2 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 2849.990 Da / Num. of mol.: 2 / Fragment: UNP Residues 615-637 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPS15, AF1P / Production host: Escherichia coli (E. coli) / References: UniProt: P42566 #2: Protein | Mass: 31229.480 Da / Num. of mol.: 2 / Fragment: UNP Residues 615-900 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: fcho1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4IJ14, UniProt: A0A0R4IA99*PLUS #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Bis-Tris propane pH, 6.0, 200 mM sodium citrate, 22% PEG 3350 and 10 mM DTT Crystals were cryopretetcted in 22% glycerol before flash cooling |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 1.60 | |||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2014 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.4→45.314 Å / Num. obs: 35451 / % possible obs: 96 % / Observed criterion σ(F): -99 / Observed criterion σ(I): -99 / Redundancy: 2.9 % / Biso Wilson estimate: 48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 8.3 | |||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.401 / Mean I/σ(I) obs: 1 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.4→45.314 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.09
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.314 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|