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Yorodumi- PDB-5wrl: Mu2 subunit of the clathrin adaptor complex AP2 in complex with I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wrl | ||||||
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Title | Mu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y628 peptide | ||||||
Components |
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Keywords | ENDOCYTOSIS / clathrin adaptor AP-2 complex subunit / peptide complex | ||||||
Function / homology | Function and homology information SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion ...SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion / positive regulation of glucagon secretion / epithelial cell migration / Gap junction degradation / Formation of annular gap junctions / 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 / clathrin-dependent endocytosis / mammary gland development / 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 / negative regulation of insulin secretion / positive regulation of glycogen biosynthetic process / phosphatidylinositol 3-kinase binding / lipid catabolic process / positive regulation of insulin receptor signaling pathway / positive regulation of phosphorylation / clathrin-coated pit / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / phosphotyrosine residue binding / SH2 domain binding / insulin-like growth factor receptor signaling pathway / ciliary basal body / protein kinase C binding / response to activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / positive regulation of glucose import / intracellular protein transport / response to insulin / insulin receptor binding / terminal bouton / receptor internalization / cytokine-mediated signaling pathway / cellular response to insulin stimulus / disordered domain specific binding / cell migration / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / insulin receptor signaling pathway / 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 / synapse / glutamatergic synapse / lipid binding / protein-containing complex binding / protein kinase binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.095 Å | ||||||
Authors | Yoneyama, Y. / Niwa, H. / Umehara, T. / Yokoyama, S. / Hakuno, F. / Takahashi, S. | ||||||
Citation | Journal: Elife / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wrl.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wrl.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/5wrl ftp://data.pdbj.org/pub/pdb/validation_reports/wr/5wrl | HTTPS FTP |
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-Related structure data
Related structure data | 5wrkC 5wrmC 1bw8S C: citing same article (ref.) S: Starting model for refinement |
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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: 31798.293 Da / Num. of mol.: 1 / Fragment: UNP residues 158-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84092 |
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#2: Protein/peptide | Mass: 969.156 Da / Num. of mol.: 1 / Fragment: UNP residues 627-634 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P35570 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 76.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.2M NaCl, 0.4M Na/K Phosphate, 0.01M DTT, 15% Glycerol, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.095→50 Å / Num. obs: 12419 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rsym value: 0.098 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.796 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.646 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BW8 Resolution: 3.095→36.427 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 29.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.095→36.427 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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