+Open data
-Basic information
Entry | Database: PDB / ID: 5iz9 | ||||||
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Title | Protein-protein interaction | ||||||
Components |
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Keywords | PROTEIN BINDING/INHIBITOR / APC / ASEF / Colon CANCER / Drug discovery / PROTEIN BINDING-INHIBITOR complex | ||||||
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 / 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 / protein kinase regulator activity / 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 / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / Deactivation of the beta-catenin transactivating complex / adherens junction / ruffle membrane / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / beta-catenin binding / 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 / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å | ||||||
Authors | Zhao, Y. / Jiang, H. / Yang, X. / Jiang, F. / Song, K. / Zhang, J. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Peptidomimetic inhibitors of APC-Asef interaction block colorectal cancer migration. Authors: Jiang, H. / Deng, R. / Yang, X. / Shang, J. / Lu, S. / Zhao, Y. / Song, K. / Liu, X. / Zhang, Q. / Chen, Y. / Chinn, Y.E. / Wu, G. / Li, J. / Chen, G. / Yu, J. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iz9.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iz9.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 5iz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iz9_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 5iz9_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 5iz9_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5iz9_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5iz9 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5iz9 | HTTPS FTP |
-Related structure data
Related structure data | 5b6gC 5iz6C 5iz8C 5izaC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39268.246 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 407-751 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 |
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#2: Protein/peptide | Mass: 655.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: 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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→51.44 Å / Num. obs: 7853 / % possible obs: 99.1 % / Redundancy: 4.4 % / Net I/σ(I): 12.45 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.48 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NMW Resolution: 2.93→51.44 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 23.027 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 79.098 Å2
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Refinement step | Cycle: 1 / Resolution: 2.93→51.44 Å
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Refine LS restraints |
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