+Open data
-Basic information
Entry | Database: PDB / ID: 2iv9 | ||||||
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Title | B2-appendage from AP2 in complex with Eps15 peptide | ||||||
Components |
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Keywords | ENDOCYTOSIS/REGULATOR / ALTERNATIVE SPLICING / ENDOCYTOSIS-REGULATOR COMPLEX / B2 / EAR / EPS15 / ADAPTOR / CALCIUM / APPENDAGE / COATED PITS / ENDOCYTOSIS / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / Golgi to endosome transport / AP-2 adaptor complex / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization ...Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / Golgi to endosome transport / AP-2 adaptor complex / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / endocytic recycling / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / aorta development / aggresome / clathrin-coated vesicle / ciliary membrane / ventricular septum development / endosomal transport / clathrin binding / positive regulation of receptor recycling / Recycling pathway of L1 / synaptic vesicle endocytosis / polyubiquitin modification-dependent protein binding / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / kidney development / EGFR downregulation / intracellular protein transport / clathrin-coated endocytic vesicle membrane / Negative regulation of MET activity / cytoplasmic side of plasma membrane / SH3 domain binding / endocytosis / endocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynapse / regulation of cell population proliferation / early endosome membrane / postsynapse / Potential therapeutics for SARS / receptor-mediated endocytosis of virus by host cell / early endosome / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / synapse / calcium ion binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ford, M.G.J. / Schmid, E.M. / McMahon, H.T. | ||||||
Citation | Journal: Plos Biol. / Year: 2006 Title: Role of the Ap2 Beta-Appendage Hub in Recruiting Partners for Clathrin-Coated Vesicle Assembly Authors: Schmid, E.M. / Ford, M.G.J. / Burtey, A. / Praefcke, G.J.K. / Peak-Chew, S.-Y. / Mills, I.G. / Benmerah, A. / Mcmahon, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iv9.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iv9.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 2iv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2iv9 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2iv9 | HTTPS FTP |
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-Related structure data
Related structure data | 2iv8C 1e42S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26899.055 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 700-937 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-15B / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P63010 #2: Protein/peptide | | Mass: 1263.311 Da / Num. of mol.: 1 / Fragment: RESIDUES 720-731 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: Q5JC29, UniProt: P42566*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 4.5 / Details: 2M AMMONIUM SULPHATE, 0.1M AMMONIUM ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 12, 2006 / Details: BENT MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.31 Å / Num. obs: 38753 / % possible obs: 97.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1 / % possible all: 89 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E42 CHAIN A Resolution: 1.9→45.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.218 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME DENSITY WAS SEEN FOR THE KEY BINDING RESIDUES AT THE EPS15 P-SHORT BINDING SITE ON MOLECULE B BUT A MODEL COULD NOT BE BUILT UNAMBIGUOSLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.31 Å
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