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Open data
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Basic information
Entry | Database: PDB / ID: 4li2 | ||||||
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Title | Crystal Structures of Lgr4 and its complex with R-spondin1 | ||||||
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![]() | Hormone Receptor/Signaling protein / LRR / Hormone Receptor-Signaling protein complex | ||||||
Function / homology | ![]() Regulation of FZD by ubiquitination / protein-hormone receptor activity / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / G protein-coupled receptor binding ...Regulation of FZD by ubiquitination / protein-hormone receptor activity / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / G protein-coupled receptor binding / Wnt signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / heparin binding / spermatogenesis / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular region / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Xenopus tropicalis![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, Y. / Rajashankar, K. / Robev, D. | ||||||
![]() | ![]() Title: Crystal structures of lgr4 and its complex with R-spondin1. Authors: Xu, K. / Xu, Y. / Rajashankar, K.R. / Robev, D. / Nikolov, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4li1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 47542.035 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN RESIDUES 23-454 / Mutation: C223S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lgr4 / Plasmid: pCDNA3.1 / Cell line (production host): HEK293 CELLS / Production host: ![]() |
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#2: Protein | Mass: 12153.070 Da / Num. of mol.: 1 / Fragment: FU 1 and FU 2 repeat residues 33-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.7 Details: 22% PEG3350, 200 mM MgCl2 and 100 mM BisTris pH 5.7, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 11577 / % possible obs: 98.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 93.49 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.704 / Net I/σ(I): 5.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LI1 Resolution: 3.19→47.613 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6885 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 35.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.17 Å2 / Biso mean: 71.1696 Å2 / Biso min: 23.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.19→47.613 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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