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Yorodumi- PDB-3qdo: Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused... -
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-Basic information
Entry | Database: PDB / ID: 3qdo | ||||||
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Title | Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused to the Gly-Gly linker followed by C-terminal (ESESKV) of GIRK3 | ||||||
Components | Sorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera | ||||||
Keywords | PROTEIN BINDING / PDZ domain / PDZ binding / GIRK3 regulation / early endosomes / brain / neurons | ||||||
Function / homology | Function and homology information response to methamphetamine hydrochloride / regulation of presynaptic membrane potential / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / inward rectifier potassium channel activity / Activation of G protein gated Potassium channels ...response to methamphetamine hydrochloride / regulation of presynaptic membrane potential / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / phosphatidylinositol-3-phosphate binding / endocytic recycling / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / endosomal transport / monoatomic ion channel complex / potassium ion import across plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / ionotropic glutamate receptor binding / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / PDZ domain binding / intracellular protein transport / Schaffer collateral - CA1 synapse / presynaptic membrane / nervous system development / early endosome membrane / early endosome / endosome / glutamatergic synapse / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Balana, B. / Kwiatkowski, W. / Choe, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Mechanism underlying selective regulation of G protein-gated inwardly rectifying potassium channels by the psychostimulant-sensitive sorting nexin 27. Authors: Balana, B. / Maslennikov, I. / Kwiatkowski, W. / Stern, K.M. / Bahima, L. / Choe, S. / Slesinger, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qdo.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qdo.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/3qdo ftp://data.pdbj.org/pub/pdb/validation_reports/qd/3qdo | HTTPS FTP |
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-Related structure data
Related structure data | 3qe1SC 3qglC S: Starting model for refinement C: citing same article (ref.) |
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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: 11344.750 Da / Num. of mol.: 1 Fragment: PDZ domain (UNP residues 39-133), GIRK-3 C-terminus (UNP residues 388-393) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mrt1, Kcnj9 / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4V4, UniProt: Q63511 |
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#2: Water | ChemComp-HOH / |
Sequence details | CHAIN A IS A CHIMERA: SNX27 PDZ DOMAIN (UNP RESIDUES 39-133), ENGINEERED LINKER, GIRK-3 C-TERMINUS ...CHAIN A IS A CHIMERA: SNX27 PDZ DOMAIN (UNP RESIDUES 39-133), ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M calcium chloride, 0.1 M HEPES, 28% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 27, 2009 / Details: mirrors |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→42.28 Å / Num. all: 7380 / Num. obs: 7380 / % possible obs: 99.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.216 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 19.4 / Num. unique all: 384 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QE1 Resolution: 1.88→42.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.514 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.074 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→42.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.881→1.93 Å / Total num. of bins used: 20
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