+Open data
-Basic information
Entry | Database: PDB / ID: 4yjl | ||||||
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Title | Crystal structure of APC-ARM in complexed with Amer1-A2 | ||||||
Components |
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Keywords | CELL ADHESION/PROTEIN BINDING / ARMADILLO-LIGAND COMPLEX / CELL ADHESION-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / beta-catenin destruction complex binding / 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 / bicellular tight junction assembly ...mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / beta-catenin destruction complex binding / 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 / bicellular tight junction assembly / pattern specification process / 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 / heart valve development / regulation of microtubule-based process / microtubule plus-end binding / 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 / regulation of canonical Wnt signaling pathway / 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 / cytoplasmic microtubule / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / adipose tissue development / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / adherens junction / bone development / 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 / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / cell migration / positive regulation of canonical Wnt signaling pathway / lamellipodium / insulin receptor signaling pathway / nervous system development / Neddylation / positive regulation of cold-induced thermogenesis / microtubule binding / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhang, Z. / Xiao, Y. / Wu, G. | ||||||
Citation | Journal: Cell Discov / Year: 2015 Title: Structures of the APC-ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners Authors: Zhang, Z. / Akyildiz, S. / Xiao, Y. / Gai, Z. / An, Y. / Behrens, J. / Wu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yjl.cif.gz | 462.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yjl.ent.gz | 378 KB | Display | PDB format |
PDBx/mmJSON format | 4yjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yjl_validation.pdf.gz | 519.4 KB | Display | wwPDB validaton report |
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Full document | 4yjl_full_validation.pdf.gz | 539.4 KB | Display | |
Data in XML | 4yjl_validation.xml.gz | 99.8 KB | Display | |
Data in CIF | 4yjl_validation.cif.gz | 147.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/4yjl ftp://data.pdbj.org/pub/pdb/validation_reports/yj/4yjl | HTTPS FTP |
-Related structure data
Related structure data | 4yjeC 4yk6C 3nmwS 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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Unit cell |
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-Components
#1: Protein | Mass: 39268.246 Da / Num. of mol.: 6 / Fragment: ARM DOMAIN, UNP RESIDUES 407-751 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25054 #2: Protein/peptide | Mass: 1520.578 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 496-508 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JTC6 #3: Chemical | ChemComp-EDO / #4: 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: 6.18 Å3/Da / Density % sol: 80.11 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2M NACL, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 335882 / % possible obs: 98.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NMW Resolution: 2.1→49.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.34 Å
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