+Open data
-Basic information
Entry | Database: PDB / ID: 4wip | ||||||
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Title | DIX domain of human Dvl2 | ||||||
Components | Segment polarity protein dishevelled homolog DVL-2 | ||||||
Keywords | SIGNALING PROTEIN / polymer signaling ubiquitin-like | ||||||
Function / homology | Function and homology information Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle ...Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / frizzled binding / PCP/CE pathway / Signaling by Hippo / WNT mediated activation of DVL / aggresome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / heart looping / outflow tract morphogenesis / lateral plasma membrane / canonical Wnt signaling pathway / positive regulation of JUN kinase activity / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / neural tube closure / RHO GTPases Activate Formins / Degradation of DVL / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / protein localization / small GTPase binding / positive regulation of DNA-binding transcription factor activity / : / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / protein-macromolecule adaptor activity / Clathrin-mediated endocytosis / heart development / regulation of cell population proliferation / cytoplasmic vesicle / nuclear body / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.691 Å | ||||||
Authors | Fiedler, M. / Bienz, M. / Madrzak, J. / Chin, J.W. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Ubiquitination of the Dishevelled DIX domain blocks its head-to-tail polymerization. Authors: Madrzak, J. / Fiedler, M. / Johnson, C.M. / Ewan, R. / Knebel, A. / Bienz, M. / Chin, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wip.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wip.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 4wip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/4wip ftp://data.pdbj.org/pub/pdb/validation_reports/wi/4wip | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 10970.392 Da / Num. of mol.: 3 / Fragment: UNP residues 13-105 / Mutation: Y27D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-11 Details (production host): https://www.embl.de/pepcore/pepcore_services/cloning/pdf/pETM-11.pdf Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus-RIL / References: UniProt: O14641 #2: Chemical | #3: 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: 3.56 Å3/Da / Density % sol: 65.49 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: grew in PEG400 (cryo condition) over night / Temp details: 19C |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 22, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.691→98.26 Å / Num. all: 13481 / Num. obs: 13481 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rpim(I) all: 0.095 / Rrim(I) all: 0.17 / Rsym value: 0.14 / Net I/av σ(I): 4.056 / Net I/σ(I): 5.9 / Num. measured all: 41191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.691→64.21 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.888 / SU B: 21.557 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.217 Å2
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Refinement step | Cycle: 1 / Resolution: 2.691→64.21 Å
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Refine LS restraints |
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