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Yorodumi- PDB-3hpm: Oxidized dimeric PICK1 PDZ C46G mutant in complex with the carbox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpm | ||||||
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Title | Oxidized dimeric PICK1 PDZ C46G mutant in complex with the carboxyl tail peptide of GluR2 | ||||||
Components | PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT | ||||||
Keywords | PROTEIN BINDING / oxidized / PDZ domain | ||||||
Function / homology | Function and homology information G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic early endosome / postsynaptic endocytic zone / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic early endosome / postsynaptic endocytic zone / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / SNAP receptor activity / dopamine transport / monoamine transport / : / dendritic spine organization / regulation of postsynaptic neurotransmitter receptor internalization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / Trafficking of GluR2-containing AMPA receptors / regulation of insulin secretion / positive regulation of receptor internalization / protein targeting / cellular response to glucose starvation / cytoskeletal protein binding / ionotropic glutamate receptor binding / ephrin receptor binding / trans-Golgi network membrane / G protein-coupled receptor binding / protein kinase C binding / intracellular protein transport / phospholipid binding / receptor tyrosine kinase binding / actin filament binding / synaptic vesicle / GTPase binding / presynaptic membrane / actin binding / dendritic spine / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / protein phosphorylation / negative regulation of gene expression / intracellular membrane-bounded organelle / signaling receptor binding / glutamatergic synapse / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / mitochondrion / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yu, J. / Shi, Y. / Zhang, M. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Redox-Regulated Lipid Membrane Binding of the PICK1 PDZ Domain. Authors: Shi, Y. / Yu, J. / Jia, Y. / Pan, L. / Shen, C. / Xia, J. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hpm.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpm.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hpm_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 3hpm_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 3hpm_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3hpm_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpm ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpm | HTTPS FTP |
-Related structure data
Related structure data | 3hpkC 2pkuS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 11533.163 Da / Num. of mol.: 2 / Fragment: PICK1 PDZ domain / Mutation: C46G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) synthetic construct (others) Gene: Pick1, rCG_60080 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GQQ2, UniProt: Q9EP80*PLUS #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS FUSED WITH PROTEASE 3C CLEAVAGE SITE AND THE C-TERMINAL TAIL 9 AMINO ACID RESIDUES ...THIS SEQUENCE IS FUSED WITH PROTEASE 3C CLEAVAGE SITE AND THE C-TERMINAL TAIL 9 AMINO ACID RESIDUES OF THE GLUR2 SUBUNIT. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEG4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Monochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.62 Å / Num. all: 4797 / Num. obs: 4797 / % possible obs: 96.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 77.041 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2 / Num. unique all: 683 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PKU Resolution: 2.8→46.62 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.891 / SU B: 46.451 / SU ML: 0.417 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.494 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→46.62 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.872 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 |
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