+Open data
-Basic information
Entry | Database: PDB / ID: 8cn3 | ||||||
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Title | hDLG1-PDZ2 in complex with a TAX1 peptide from HTLV-1 | ||||||
Components |
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Keywords | PROTEIN BINDING / HTLV-1 / Tax-1 / hDLG1 / PBM / protein protein 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 / negative regulation of p38MAPK cascade ...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 / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / 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 / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / node of Ranvier / 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 / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / 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 / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / 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 / intercalated disc / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / 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 / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / 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) Human T-cell lymphotrophic virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Maseko, S. / Sogues, A. / Volkov, A. / Remaut, H. / Twizere, J.C. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Antiviral Res. / Year: 2023 Title: Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Authors: Maseko, S.B. / Brammerloo, Y. / Van Molle, I. / Sogues, A. / Martin, C. / Gorgulla, C. / Plant, E. / Olivet, J. / Blavier, J. / Ntombela, T. / Delvigne, F. / Arthanari, H. / El Hajj, H. / ...Authors: Maseko, S.B. / Brammerloo, Y. / Van Molle, I. / Sogues, A. / Martin, C. / Gorgulla, C. / Plant, E. / Olivet, J. / Blavier, J. / Ntombela, T. / Delvigne, F. / Arthanari, H. / El Hajj, H. / Bazarbachi, A. / Van Lint, C. / Salehi-Ashtiani, K. / Remaut, H. / Ballet, S. / Volkov, A.N. / Twizere, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cn3.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cn3.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cn3 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cn3 | HTTPS FTP |
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-Related structure data
Related structure data | 8cn1C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12381.181 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12959 | ||
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#2: Protein | Mass: 12383.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12959 | ||
#3: Protein/peptide | Mass: 476.477 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Human T-cell lymphotrophic virus type 1 (strain ATK) #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: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 5.5, 0.075M (NH4)2SO4, 24% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.706→40.26 Å / Num. obs: 4059 / % possible obs: 90.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.15 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.089 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.706→2.824 Å / Num. unique obs: 203 / CC1/2: 0.803 / Rpim(I) all: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→40.26 Å / SU ML: 0.2956 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3182 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.08 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→40.26 Å
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Refine LS restraints |
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