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Yorodumi- PDB-7pc3: The second PDZ domain of DLG1 complexed with the PDZ-binding moti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pc3 | ||||||
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Title | The second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone | ||||||
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 / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding ...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 / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / membrane raft organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / hard palate development / establishment of centrosome localization / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / myelin sheath adaxonal region / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / cadherin binding involved in cell-cell adhesion / smooth muscle tissue development / Schmidt-Lanterman incisure / vesicle budding from membrane / bicellular tight junction assembly / cornified envelope / positive regulation of potassium ion transport / node of Ranvier / plasma membrane protein complex / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / collagen fibril organization / endothelial cell proliferation / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / positive regulation of low-density lipoprotein receptor activity / regulation of myelination / epithelial cell apoptotic process / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / positive regulation of receptor recycling / negative regulation of G1/S transition of mitotic cell cycle / phosphatidylserine binding / positive regulation of actin filament polymerization / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of exocytosis / phosphoprotein phosphatase activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Long-term potentiation / immunological synapse / basement membrane / regulation of neurogenesis / intercalated disc / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Smooth Muscle Contraction / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / fibrinolysis / actin filament polymerization / regulation of membrane potential / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HTLV-1 subtype A (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Cousido-Siah, A. / Trave, G. / Gogl, G. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: A scalable strategy to solve structures of PDZ domains and their complexes. Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pc3.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pc3.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 7pc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/7pc3 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/7pc3 | HTTPS FTP |
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-Related structure data
Related structure data | 7pc4C 7pc5C 7pc7C 7pc8C 7pc9C 7pcbC 7qqlC 7qqmC 7qqnC 2x7zS 5n7dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 46970.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q12959, UniProt: P07355 |
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#2: Protein/peptide | Mass: 1264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label Source: (synth.) HTLV-1 subtype A (virus) / References: UniProt: P03409 |
-Non-polymers , 4 types, 406 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.553 Å / Num. obs: 36311 / % possible obs: 99.2 % / Redundancy: 13.37 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 12.58 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2616 / CC1/2: 0.645 / Rrim(I) all: 1.605 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N7D, 2X7Z Resolution: 1.95→46.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.94 Å2 / Biso mean: 30.8243 Å2 / Biso min: 11.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→46.553 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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