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Yorodumi- PDB-2rqu: Solution structure of the complex between the DDEF1 SH3 domain an... -
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-Basic information
Entry | Database: PDB / ID: 2rqu | ||||||
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Title | Solution structure of the complex between the DDEF1 SH3 domain and the APC SAMP1 motif | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH3 domain / GAP / SAMP motif / Tumor suppressor / Cell junction / Disease mutation / Phosphoprotein / Wnt signaling pathway | ||||||
Function / homology | Function and homology information positive regulation of membrane tubulation / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome ...positive regulation of membrane tubulation / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / protein localization to cilium / beta-catenin destruction complex / regulation of microtubule-based process / heart valve development / 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 / podosome / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / regulation of postsynapse organization / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / phosphatidylserine binding / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / mitotic cytokinesis / cilium assembly / lateral plasma membrane / bicellular tight junction / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / trans-Golgi network membrane / Deactivation of the beta-catenin transactivating complex / adherens junction / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / kinetochore / beta-catenin binding / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / cell migration / Ovarian tumor domain proteases / insulin receptor signaling pathway / lamellipodium / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / dendritic spine / cell adhesion / positive regulation of cell migration / cadherin binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / Golgi membrane / centrosome / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Kaieda, S. / Matsui, C. / Mimori-Kiyosue, Y. / Ikegami, T. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-homology 3 domain. Authors: Kaieda, S. / Matsui, C. / Mimori-Kiyosue, Y. / Ikegami, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rqu.cif.gz | 493.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rqu.ent.gz | 412.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/2rqu ftp://data.pdbj.org/pub/pdb/validation_reports/rq/2rqu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7066.801 Da / Num. of mol.: 1 / Fragment: UNP residues 1069-1129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULH1 |
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#2: Protein/peptide | Mass: 2050.511 Da / Num. of mol.: 1 / Fragment: UNP residues 1578-1596 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Production host: Escherichia coli (E. coli) / References: UniProt: P25054 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 7.2 / Pressure: ambient / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1 |