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- PDB-5wrk: Mu2 subunit of the clathrin adaptor complex AP2 in complex with I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wrk | ||||||
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Title | Mu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y608 peptide | ||||||
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![]() | ENDOCYTOSIS / clathrin adaptor AP-2 complex subunit / peptide complex | ||||||
Function / homology | ![]() SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / Interleukin-7 signaling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK ...SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / Interleukin-7 signaling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion / positive regulation of glucagon secretion / Gap junction degradation / Formation of annular gap junctions / epithelial cell migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Signal attenuation / WNT5A-dependent internalization of FZD4 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / vesicle budding from membrane / mammary gland development / clathrin-dependent endocytosis / insulin receptor complex / positive regulation of glucose metabolic process / signal sequence binding / transmembrane receptor protein tyrosine kinase adaptor activity / cellular response to angiotensin / RAF/MAP kinase cascade / negative regulation of protein localization to plasma membrane / response to caffeine / positive regulation of mesenchymal cell proliferation / cellular response to fatty acid / low-density lipoprotein particle receptor binding / positive regulation of epithelial cell migration / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / protein localization to nucleus / positive regulation of glycogen biosynthetic process / negative regulation of insulin secretion / phosphatidylinositol 3-kinase binding / lipid catabolic process / positive regulation of insulin receptor signaling pathway / clathrin-coated pit / positive regulation of phosphorylation / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of insulin receptor signaling pathway / phosphotyrosine residue binding / SH2 domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / ciliary basal body / response to activity / caveola / positive regulation of glucose import / protein kinase C binding / intracellular protein transport / insulin-like growth factor receptor binding / insulin receptor binding / response to insulin / terminal bouton / receptor internalization / cytokine-mediated signaling pathway / cellular response to insulin stimulus / disordered domain specific binding / signaling receptor complex adaptor activity / cell migration / insulin receptor signaling pathway / protein-macromolecule adaptor activity / cytoplasmic vesicle / postsynapse / regulation of gene expression / protein-containing complex assembly / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein domain specific binding / intracellular membrane-bounded organelle / glutamatergic synapse / lipid binding / synapse / protein-containing complex binding / protein kinase binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoneyama, Y. / Niwa, H. / Umehara, T. / Yokoyama, S. / Hakuno, F. / Takahashi, S. | ||||||
![]() | ![]() Title: IRS-1 acts as an endocytic regulator of IGF-I receptor to facilitate sustained IGF signaling Authors: Yoneyama, Y. / Lanzerstorfer, P. / Niwa, H. / Umehara, T. / Shibano, T. / Yokoyama, S. / Chida, K. / Weghuber, J. / Hakuno, F. / Takahashi, S.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.5 KB | Display | ![]() |
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PDB format | ![]() | 92.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wrlC ![]() 5wrmC ![]() 1bw8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30911.723 Da / Num. of mol.: 1 / Fragment: UNP residues 158-223,UNP residues 261-435 Source method: isolated from a genetically manipulated source Details: B chain is a part of A chain for which residue names and residue numbers were not determined due to insufficient electron density Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 838.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#3: Chemical | Sequence details | THE ELECTRON DENSITY OF RESIDUES A224-A260 IS WEAK. FIVE RESIDUES WERE PLACED BUT THEIR RESIDUE ...THE ELECTRON DENSITY OF RESIDUES A224-A260 IS WEAK. FIVE RESIDUES WERE PLACED BUT THEIR RESIDUE NUMBERS A227-A231 ARE NOT CONCLUSIVE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.3 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.4M Na formate, 0.05M NiCl, 0.1M Na acetate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.624→50 Å / Num. obs: 20035 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rsym value: 0.075 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.433 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BW8 Resolution: 2.62→43.8 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 26.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→43.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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