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Yorodumi- PDB-5fpi: Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fpi | ||||||
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Title | Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) complexed with Integrin alpha4 internalisation peptide QYKSILQE | ||||||
Components |
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Keywords | ENDOCYTOSIS / CLATHRIN ADAPTOR | ||||||
Function / homology | Function and homology information clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / negative regulation of protein homodimerization activity / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / Gap junction degradation / Formation of annular gap junctions ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / negative regulation of protein homodimerization activity / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / 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 / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / positive regulation of leukocyte tethering or rolling / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / axonogenesis involved in innervation / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / protein antigen binding / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / leukocyte tethering or rolling / clathrin-dependent endocytosis / positive regulation of endothelial cell apoptotic process / RUNX3 Regulates Immune Response and Cell Migration / signal sequence binding / negative regulation of protein localization to plasma membrane / heterotypic cell-cell adhesion / integrin complex / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / neuron projection extension / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / low-density lipoprotein particle receptor binding / receptor clustering / endodermal cell differentiation / cellular response to cytokine stimulus / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / fibronectin binding / synaptic vesicle endocytosis / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / clathrin-coated pit / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / B cell differentiation / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / intracellular protein transport / terminal bouton / receptor internalization / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / disordered domain specific binding / synaptic vesicle / growth cone / cytoplasmic vesicle / Potential therapeutics for SARS / protein-containing complex assembly / transmembrane transporter binding / postsynapse / membrane => GO:0016020 / cell adhesion / external side of plasma membrane / focal adhesion / neuronal cell body / lipid binding / glutamatergic synapse / synapse / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Owen, D.J. / Evans, P.R. / Ivaska, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Selective Integrin Endocytosis is Driven by Alpha Chain:Ap2 Interactions Authors: De Franceschi, N. / Arjonen, A. / Elkhatib, N. / Denessiouk, K. / Wrobel, A.G. / Wilson, T.A. / Pouwels, J. / Montagnac, G. / Owen, D.J. / Ivaska, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpi.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpi.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fpi_validation.pdf.gz | 415.4 KB | Display | wwPDB validaton report |
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Full document | 5fpi_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 5fpi_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5fpi_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpi ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpi | HTTPS FTP |
-Related structure data
Related structure data | 1bxxS 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: 51044.113 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PLASMID / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P84092 |
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#2: Protein/peptide | Mass: 1009.134 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL PEPTIDE, RESIDUES 150-157 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8IU71, UniProt: P13612*PLUS |
#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: 3.26 Å3/Da / Density % sol: 62.24 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 2.2M NACL, 0.4M NAKPHOSPHATE, 20% V/V GLYCEROL, 0.1M MES PH6.5, 5MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54182 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2015 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→74 Å / Num. obs: 17034 / % possible obs: 97.2 % / Observed criterion σ(I): -9.9 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 80.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXX Resolution: 2.77→108.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.982 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.116 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→108.82 Å
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