+Open data
-Basic information
Entry | Database: PDB / ID: 4qxf | ||||||
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Title | crystal structure of human LGR4 and Rspo1 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ligand-receptor complex / LRR repeats / Beta-Hairpins / Glucosylation / Cell Membrane | ||||||
Function / homology | Function and homology information metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling ...metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling / G protein-coupled peptide receptor activity / digestive tract development / negative regulation of cold-induced thermogenesis / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / hormone-mediated signaling pathway / G protein-coupled receptor activity / G protein-coupled receptor binding / circadian regulation of gene expression / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / spermatogenesis / positive regulation of protein phosphorylation / signaling receptor binding / innate immune response / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Eptatretus burgeri (inshore hagfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Xu, J.G. / Huang, C. / Zhou, Y. / Zhu, Y. | ||||||
Citation | Journal: TO BE PUBLISHED Title: crystal structure of human LGR4 and Rspo1 Authors: Xu, J.G. / Huang, C. / Zhou, Y. / Zhu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxf.cif.gz | 306.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxf.ent.gz | 250.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxf ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxf | HTTPS FTP |
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-Related structure data
Related structure data | 4qxeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33151.766 Da / Num. of mol.: 2 / Fragment: UNP residues 27-252, UNP residues 128-200 / Mutation: D75G Source method: isolated from a genetically manipulated source Details: chimera of (Leucine-rich repeat-containing G-protein coupled receptor 4 and Variable lymphocyte receptor B) Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish) Gene: GPR48, LGR4, VLRB / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9BXB1, UniProt: Q4G1L2 #2: Protein | Mass: 11185.049 Da / Num. of mol.: 2 / Fragment: UNP residues 34-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RSPO1 / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q2MKA7 #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: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97925 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. all: 44255 / Num. obs: 43609 / % possible obs: 98.54 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QXE Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.743 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.21 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.173 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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