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Yorodumi- PDB-2bp5: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -
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-Basic information
Entry | Database: PDB / ID: 2bp5 | ||||||
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Title | MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH NON-CANONICAL INTERNALIZATION PEPTIDE VEDYEQGLSG | ||||||
Components |
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Keywords | ENDOCYTOSIS / ADAPTOR / COATED PITS / ENDOCYTOSIS-EXOCYTOSIS / ENDOCYTOSIS/EXOCYTOSIS / PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information Platelet homeostasis / Elevation of cytosolic Ca2+ levels / sensory perception of touch / ligand-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...Platelet homeostasis / Elevation of cytosolic Ca2+ levels / sensory perception of touch / ligand-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / 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 / purinergic nucleotide receptor signaling pathway / positive regulation of microglial cell migration / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / negative regulation of cardiac muscle hypertrophy / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / response to fluid shear stress / ligand-gated calcium channel activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / ATP-gated ion channel activity / regulation of chemotaxis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / inorganic cation transmembrane transport / negative regulation of protein localization to plasma membrane / relaxation of cardiac muscle / cellular response to zinc ion / positive regulation of endothelial cell chemotaxis / cellular response to ATP / positive regulation of calcium ion transport into cytosol / low-density lipoprotein particle receptor binding / response to ATP / behavioral response to pain / Trafficking of GluR2-containing AMPA receptors / membrane depolarization / positive regulation of receptor internalization / synaptic vesicle endocytosis / regulation of cardiac muscle contraction / response to axon injury / neuronal action potential / positive regulation of blood vessel endothelial cell migration / positive regulation of calcium-mediated signaling / regulation of sodium ion transport / clathrin-coated pit / monoatomic ion transmembrane transport / sensory perception of pain / nitric oxide biosynthetic process / excitatory postsynaptic potential / response to ischemia / calcium ion transmembrane transport / apoptotic signaling pathway / intracellular protein transport / terminal bouton / receptor internalization / regulation of blood pressure / vasodilation / calcium ion transport / disordered domain specific binding / apical part of cell / cell junction / cell body / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / transmembrane transporter binding / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / copper ion binding / lysosomal membrane / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / lipid binding / synapse / dendrite / perinuclear region of cytoplasm / signal transduction / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Royle, S.J. / Evans, P.R. / Owen, D.J. / Murrell-Lagnado, R.D. | ||||||
Citation | Journal: J.Cell.Sci / Year: 2005 Title: Non-Canonical Yxxg-Phi Endocytic Motifs: Recognition by Ap2 and Preferential Utilization in P2X4 Receptors. Authors: Royle, S.J. / Qureshi, O.S. / Bobanovic, L.K. / Evans, P.R. / Owen, D.J. / Murrell-Lagnado, R.D. | ||||||
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 | 2bp5.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bp5.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bp5_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 2bp5_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 2bp5_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2bp5_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp5 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp5 | 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 on special symmetry positions |
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Details | ALTHOUGH CHAIN M IS A DOMAIN OF A LARGER PROTEINWHICH EXISTS IN ITS NATIVE STATE AS A TETRAMER, THISENTRY IS ANNOTATED AS A DIMER AS IT IS IN COMPLEXWITH A SMALL PEPTIDE (CHAIN P). |
-Components
#1: Protein | Mass: 49726.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P84092 |
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#2: Protein/peptide | Mass: 1096.103 Da / Num. of mol.: 1 / Fragment: RESIDUES 375-384 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P51577 |
#3: Water | ChemComp-HOH / |
Compound details | FUNCTION: COMPONENT OF THE ADAPTOR COMPLEXES WHICH LINK CLATHRIN TO RECEPTORS IN COATED VESICLES. ...FUNCTION: COMPONENT OF THE ADAPTOR COMPLEXES WHICH LINK CLATHRIN TO RECEPTORS IN COATED VESICLES. CLATHRIN-ASSOCIATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 60 % / Description: ISOMORPHOUS CRYSTAL TO 1BXX |
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Crystal grow | Temperature: 289 K / pH: 7.1 Details: 2.2M NACL, 0.4M NA/K PHOSPHATE PH 7.1, 10MM DTT, 0.1M MES, 15% GLYCEROL, 16 DEGREES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 30, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→23.6 Å / Num. obs: 16497 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 36 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXX Resolution: 2.8→105.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.807 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.266 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→105.41 Å
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