+Open data
-Basic information
Entry | Database: PDB / ID: 3rl8 | ||||||
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Title | Crystal structure of hDLG1-PDZ2 complexed with APC | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/SIGNALING PROTEIN / PDZ-ligand complex / MEMBRANE PROTEIN-SIGNALING PROTEIN complex | ||||||
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 / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development ...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 / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development / negative regulation of cell cycle G1/S phase transition / 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 / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / positive regulation of protein localization to centrosome / smooth muscle tissue development / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / positive regulation of potassium ion transport / negative regulation of microtubule depolymerization / regulation of ventricular cardiac muscle cell action potential / negative regulation of cyclin-dependent protein serine/threonine kinase activity / amyloid precursor protein metabolic process / node of Ranvier / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / heart valve development / protein-containing complex localization / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Assembly and cell surface presentation of NMDA receptors / endothelial cell proliferation / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / cell fate specification / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / endocardial cushion morphogenesis / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / mitotic spindle assembly checkpoint signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / phosphoprotein phosphatase activity / Long-term potentiation / mitotic cytokinesis / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Zhang, Z. / Li, H. / Wu, G. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Molecular basis for the recognition of adenomatous polyposis coli by the Discs Large 1 protein. Authors: Zhang, Z. / Li, H. / Chen, L. / Lu, X. / Zhang, J. / Xu, P. / Lin, K. / Wu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rl8.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rl8.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/3rl8 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/3rl8 | HTTPS FTP |
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-Related structure data
Related structure data | 3rl7C 1zokS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 317 - 405 / Label seq-ID: 12 - 100
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-Components
#1: Protein | Mass: 11460.296 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 315-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12959 #2: Protein/peptide | | Mass: 1207.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P25054 #3: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.65 % / Mosaicity: 0.279 ° |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Nov 30, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→85.38 Å / Num. obs: 30730 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Χ2: 1.002 / Net I/σ(I): 17.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZOK Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 11.851 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 max: 160.64 Å2 / Biso mean: 38.8215 Å2 / Biso min: 11.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 653 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.201→2.258 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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