+Open data
-Basic information
Entry | Database: PDB / ID: 2iv8 | ||||||
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Title | beta appendage in complex with b-arrestin peptide | ||||||
Components |
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Keywords | ENDOCYTOSIS/REGULATOR / ENDOCYTOSIS-REGULATOR COMPLEX / SENSORY TRANSDUCTION / RECEPTOR / COATED PITS / ADAPTOR COMPLEX-REGULATOR | ||||||
Function / homology | Function and homology information angiotensin receptor binding / 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 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Activation of SMO / Retrograde neurotrophin signalling ...angiotensin receptor binding / 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 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Activation of SMO / Retrograde neurotrophin signalling / negative regulation of interleukin-8 production / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / arrestin family protein binding / signal sequence binding / Nef Mediated CD4 Down-regulation / G protein-coupled receptor internalization / endolysosome membrane / enzyme inhibitor activity / aorta development / ventricular septum development / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / negative regulation of NF-kappaB transcription factor activity / clathrin binding / Golgi Associated Vesicle Biogenesis / negative regulation of Notch signaling pathway / stress fiber assembly / pseudopodium / Recycling pathway of L1 / negative regulation of interleukin-6 production / positive regulation of receptor internalization / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / vesicle-mediated transport / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / MHC class II antigen presentation / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / clathrin-coated endocytic vesicle membrane / kidney development / G protein-coupled receptor binding / intracellular protein transport / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / cytoplasmic side of plasma membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Cargo recognition for clathrin-mediated endocytosis / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Clathrin-mediated endocytosis / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / presynapse / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / postsynapse / positive regulation of ERK1 and ERK2 cascade / nuclear body / Ub-specific processing proteases / protein ubiquitination / positive regulation of protein phosphorylation / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / glutamatergic synapse / regulation of transcription by RNA polymerase II / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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. / Mills, I.G. / Benmerah, A. / Mcmahon, H.T. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iv8.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iv8.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 2iv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iv8_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 2iv8_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 2iv8_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2iv8_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2iv8 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2iv8 | HTTPS FTP |
-Related structure data
Related structure data | 2iv9C 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.: 1 / Fragment: RESIDUES 700-937 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Plasmid: PET-15B / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P63010 | ||
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#2: Protein/peptide | Mass: 2417.651 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-402 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49407 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 7.4 Details: 0.2M MG FORMATE 30% PEG 3350 OTHER REMARKS: THIS WAS THE ONLY CRYSTAL OBTAINED DESPITE HEROIC ATTEMPTS. THE CRYSTAL WAS HIGHLY MOSAIC, AND EPITAXIALLY SPLIT, LIMITING THE AMOUNT OF DATA ...Details: 0.2M MG FORMATE 30% PEG 3350 OTHER REMARKS: THIS WAS THE ONLY CRYSTAL OBTAINED DESPITE HEROIC ATTEMPTS. THE CRYSTAL WAS HIGHLY MOSAIC, AND EPITAXIALLY SPLIT, LIMITING THE AMOUNT OF DATA WHICH COULD BE COLLECTED., pH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.78 Å / Num. obs: 4759 / % possible obs: 70.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5 / % possible all: 63.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E42, CHAIN A Resolution: 2.8→19.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.781 / SU B: 23.134 / SU ML: 0.455 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.788 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.78 Å
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Refine LS restraints |
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