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Yorodumi- PDB-2pr9: Mu2 adaptin subunit (AP50) of AP2 adaptor (second domain), comple... -
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-Basic information
Entry | Database: PDB / ID: 2pr9 | ||||||
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Title | Mu2 adaptin subunit (AP50) of AP2 adaptor (second domain), complexed with GABAA receptor-gamma2 subunit-derived internalization peptide DEEYGYECL | ||||||
Components |
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Keywords | ENDOCYTOSIS / adaptor / internalization peptide complex / inhibitory neurotransmitter receptor | ||||||
Function / homology | Function and homology information GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / response to anesthetic / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 ...GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / response to anesthetic / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / inhibitory synapse / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / GABA receptor complex / Recycling pathway of L1 / cellular response to histamine / Cargo recognition for clathrin-mediated endocytosis / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of synaptic vesicle endocytosis / inhibitory synapse assembly / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride transport / cellular response to zinc ion / low-density lipoprotein particle receptor binding / chloride channel activity / adult behavior / positive regulation of receptor internalization / Trafficking of GluR2-containing AMPA receptors / chloride channel complex / regulation of postsynaptic membrane potential / synaptic vesicle endocytosis / transmembrane transporter complex / negative regulation of protein localization to plasma membrane / clathrin-coated pit / GABA-ergic synapse / chloride transmembrane transport / dendrite membrane / post-embryonic development / intracellular protein transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / terminal bouton / receptor internalization / disordered domain specific binding / synaptic vesicle / cytoplasmic vesicle / protein-containing complex assembly / chemical synaptic transmission / response to ethanol / transmembrane transporter binding / postsynapse / neuron projection / axon / lipid binding / glutamatergic synapse / synapse / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Vahedi-Faridi, A. / Haucke, V. / Kittler, J.T. / Kukhtina, V. / Moss, S.J. / Saenger, W. / Chen, G.-J. / Tretter, V. / Smith, K. / Yan, Z. ...Vahedi-Faridi, A. / Haucke, V. / Kittler, J.T. / Kukhtina, V. / Moss, S.J. / Saenger, W. / Chen, G.-J. / Tretter, V. / Smith, K. / Yan, Z. / McAinsh, K. / Arancibia-Carcamo, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Regulation of synaptic inhibition by phospho-dependent binding of the AP2 complex to a YECL motif in the GABAA receptor gamma2 subunit. Authors: Kittler, J.T. / Chen, G. / Kukhtina, V. / Vahedi-Faridi, A. / Gu, Z. / Tretter, V. / Smith, K.R. / McAinsh, K. / Arancibia-Carcamo, I.L. / Saenger, W. / Haucke, V. / Yan, Z. / Moss, S.J. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pr9.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pr9.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pr9_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 2pr9_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 2pr9_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2pr9_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2pr9 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2pr9 | HTTPS FTP |
-Related structure data
Related structure data | 1bw8S 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: 34100.840 Da / Num. of mol.: 1 / Fragment: second domain (residues 158-435) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Plasmid: pET-28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P84092 |
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#2: Protein/peptide | Mass: 1235.232 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. This sequence occurs naturally in mouse and rat. References: UniProt: P18508 |
#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: 4.86 Å3/Da / Density % sol: 74.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.0 M sodium formate, 0.1 M Na-acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 22817 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 66.389 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.14 |
Reflection shell | Resolution: 2.5→2.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1 / Num. unique all: 3053 / % possible all: 68.9 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BW8 Resolution: 2.51→9.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.237 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / 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: 52.027 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→9.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.512→2.573 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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