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Yorodumi- PDB-2x7z: Crystal Structure of the SAP97 PDZ2 I342W C378A mutant protein domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x7z | ||||||
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Title | Crystal Structure of the SAP97 PDZ2 I342W C378A mutant protein domain | ||||||
Components | DISKS LARGE HOMOLOG 1 | ||||||
Keywords | STRUCTURAL PROTEIN / SH3 DOMAIN / PHOSPHOPROTEIN / SYNAPTIC PROTEIN / HOST-VIRUS INTERACTION | ||||||
Function / homology | Function and homology information regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / guanylate kinase activity / NrCAM interactions / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / amyloid precursor protein metabolic process / node of Ranvier / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / protein-containing complex localization / Assembly and cell surface presentation of NMDA receptors / endothelial cell proliferation / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / intercalated disc / potassium channel regulator activity / lateral plasma membrane / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / cytoskeletal protein binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / adherens junction / sarcolemma / neuromuscular junction / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / kinase binding / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / regulation of cell shape / chemical synaptic transmission / RAF/MAP kinase cascade / basolateral plasma membrane / microtubule / transmembrane transporter binding / molecular adaptor activity / neuron projection / cadherin binding / membrane raft / apical plasma membrane / glutamatergic synapse / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular exosome / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Haq, S.R. / Jurgens, M.C. / Chi, C.N. / Elfstrom, L. / Koh, C.S. / Selmer, M. / Gianni, S. / Jemth, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: The Plastic Energy Landscape of Protein Folding: A Triangular Folding Mechanism with an Equilibrium Intermediate for a Small Protein Domain. Authors: Haq, S.R. / Jurgens, M.C. / Chi, C.N. / Elfstrom, L. / Koh, C.S. / Selmer, M. / Gianni, S. / Jemth, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x7z.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x7z.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7z ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7z | HTTPS FTP |
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-Related structure data
Related structure data | 2awuS 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: 10484.023 Da / Num. of mol.: 1 / Fragment: PDZ2 DOMAIN, RESIDUES 260-356 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-SAP97-PDZ2-I342W-C378A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q12959 |
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#2: Chemical | ChemComp-NH4 / |
#3: Chemical | ChemComp-IMD / |
#4: 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: 3.37 Å3/Da / Density % sol: 63.5 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 8.4 Details: VAPOR DIFFUSION, 100MM TRIS-HCL PH 8.4, 2.4M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Jan 21, 2009 / Details: MIRRORS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.9 Å / Num. obs: 10153 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 15.4 / % possible all: 96.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AWU Resolution: 2→29.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.174 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: 16.951 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.69 Å
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