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- PDB-5fww: Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fww | ||||||
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Title | Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) | ||||||
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Function / homology | ![]() negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation ...negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation / Wnt-Frizzled-LRP5/6 complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zebisch, M. / Jackson, V.A. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf Authors: Zebisch, M. / Jackson, V.A. / Zhao, Y. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.1 KB | Display | ![]() |
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PDB format | ![]() | 162.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 70093.898 Da / Num. of mol.: 1 / Fragment: PE3PE4, RESIDUES 630-1246 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 32728.531 Da / Num. of mol.: 1 / Fragment: ECD, RESIDUES 30-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 9607.076 Da / Num. of mol.: 1 / Fragment: CRD2, RESIDUES 182-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow![]() | pH: 7.5 / Details: 20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.5→67.68 Å / Num. obs: 8070 / % possible obs: 51.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 4.6 |
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Processing
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Refinement | Method to determine structure![]() Starting model: NONE Resolution: 3.5→135.36 Å / Cor.coef. Fo:Fc: 0.763 / Cor.coef. Fo:Fc free: 0.701 / Cross valid method: THROUGHOUT / ESU R Free: 1.576 / 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: 58.615 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→135.36 Å
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