+Open data
-Basic information
Entry | Database: PDB / ID: 3au3 | ||||||
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Title | Crystal structure of armadillo repeat domain of APC | ||||||
Components | Adenomatous polyposis coli proteinFamilial adenomatous polyposis | ||||||
Keywords | SIGNALING PROTEIN / Armadillo repeat / signal transduction / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / 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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity ...APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / 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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of microtubule depolymerization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / microtubule plus-end binding / heart valve development / regulation of microtubule-based process / protein kinase regulator activity / 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 / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / dynein complex binding / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / 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 / Ovarian tumor domain proteases / cell migration / 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 / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2011 Title: Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of sam68 Authors: Morishita, E.C. / Murayama, K. / Kato-Murayama, M. / Ishizuka-Katsura, Y. / Tomabechi, Y. / Hayashi, T. / Terada, T. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3au3.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3au3.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 3au3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3au3 ftp://data.pdbj.org/pub/pdb/validation_reports/au/3au3 | HTTPS FTP |
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-Related 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: 38678.207 Da / Num. of mol.: 1 / Fragment: Armadillo repeat, UNP residues 396-732 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Plasmid: pCR2.1 / Production host: cell-free protein synthesis (unknown) / References: UniProt: P25054 |
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#2: 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: 3.02 Å3/Da / Density % sol: 59.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100mM sodium acetate, 1.25M lithium citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97897, 0.97934, 0.964 | ||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 21, 2009 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 27064 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.077 / Net I/σ(I): 29.5 | ||||||||||||
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.623 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→49.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1779639.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4731 Å2 / ksol: 0.375332 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→49.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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