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- PDB-4ufr: Structure of the ectodomain of LGR5 in complex with R-spondin-2 (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ufr | ||||||
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Title | Structure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2) | ||||||
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![]() | SIGNALING PROTEIN / WNT / LGR / RSPO | ||||||
Function / homology | ![]() trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / embryonic forelimb morphogenesis ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / epithelial tube branching involved in lung morphogenesis / bone mineralization / inner ear development / hair follicle development / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / cell surface / extracellular region / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zebisch, M. / Jones, E.Y. | ||||||
![]() | ![]() Title: Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3. Authors: Zebisch, M. / 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 | ![]() | 449.3 KB | Display | ![]() |
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PDB format | ![]() | 375.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.5 KB | Display | ![]() |
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Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 54052.348 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544 Source method: isolated from a genetically manipulated source Details: UNSTRUCTURED LOOP REPLACED WITH SHORT LINKER, A488-H537 TO NGNNGD Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 13946.869 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 39-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Sugar | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 25 %W/V PEG3350, 0.200 M LITHIUM SULPHATE, 0.100 M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→69 Å / Num. obs: 62167 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8 |
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Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→110.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 23.344 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.229 / 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: 59.664 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→110.67 Å
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