+Open data
-Basic information
Entry | Database: PDB / ID: 4yje | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of APC-ARM in complexed with Amer1-A1 | ||||||
Components |
| ||||||
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 / positive regulation of pseudopodium assembly / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / negative regulation of microtubule depolymerization / positive regulation of protein localization to centrosome ...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 / positive regulation of pseudopodium assembly / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / negative regulation of microtubule depolymerization / 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 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 / 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 / protein kinase regulator activity / 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 / mitotic spindle assembly checkpoint signaling / dynein complex binding / Apoptotic cleavage of cellular proteins / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / adipose tissue development / phosphatidylinositol-4,5-bisphosphate binding / bone development / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Wnt signaling pathway / kinetochore / beta-catenin binding / ruffle membrane / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / positive regulation of cold-induced thermogenesis / Ovarian tumor domain proteases / cell migration / lamellipodium / insulin receptor signaling pathway / Neddylation / nervous system development / microtubule binding / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yje.cif.gz | 158.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yje.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 4yje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yje_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4yje_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 4yje_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4yje_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/4yje ftp://data.pdbj.org/pub/pdb/validation_reports/yj/4yje | HTTPS FTP |
-Related structure data
Related structure data | 4yjlC 4yk6C 3nmwS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39268.246 Da / Num. of mol.: 1 / 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: 1119.247 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 325-335 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JTC6 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 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: 1.9→50 Å / Num. obs: 27310 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.366 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NMW Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.873 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 22.26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|