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Yorodumi- PDB-5lnp: Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lnp | ||||||
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Title | Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction | ||||||
Components | (Segment polarity protein dishevelled homolog DVL-2) x 2 | ||||||
Keywords | SIGNALING PROTEIN / Dishevelled / DEP domain / WNT signalling | ||||||
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 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / 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 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / frizzled binding / PCP/CE pathway / WNT mediated activation of DVL / Signaling by Hippo / 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 / canonical Wnt signaling pathway / lateral plasma membrane / 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 / protein-macromolecule adaptor activity / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / regulation of cell population proliferation / heart development / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Renko, M. / Gammons, M.V. / Bienz, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2016 Title: Wnt Signalosome Assembly by DEP Domain Swapping of Dishevelled. Authors: Gammons, M.V. / Renko, M. / Johnson, C.M. / Rutherford, T.J. / Bienz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lnp.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lnp.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/5lnp ftp://data.pdbj.org/pub/pdb/validation_reports/ln/5lnp | 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: 10862.361 Da / Num. of mol.: 3 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14641 #2: Protein | | Mass: 10846.361 Da / Num. of mol.: 1 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14641 #3: Chemical | ChemComp-SO4 / | #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: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, pH=6.5 0.1 M NaCl 0.1 M Li2SO4 23 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.99→42.02 Å / Num. obs: 29398 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.3 | |||||||||||||||
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2884 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished model Resolution: 1.99→42.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.387 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.899 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→42.02 Å
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