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Yorodumi- PDB-4ufs: Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the... -
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-Basic information
Entry | Database: PDB / ID: 4ufs | ||||||
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Title | Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / WNT / LGR / RSPO | ||||||
Function / homology | Function and homology information trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / protein-hormone receptor activity / Regulation of FZD by ubiquitination ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / frizzled binding / embryonic forelimb morphogenesis / regulation of canonical Wnt signaling pathway / embryonic hindlimb morphogenesis / limb development / epithelial tube branching involved in lung morphogenesis / negative regulation of Wnt signaling pathway / bone mineralization / plasma membrane => GO:0005886 / inner ear development / hair follicle development / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / trans-Golgi network membrane / stem cell proliferation / G protein-coupled receptor activity / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / osteoblast differentiation / ubiquitin-protein transferase activity / transmembrane signaling receptor activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / protein ubiquitination / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / cell surface / extracellular region / nucleoplasm / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å | ||||||
Authors | Zebisch, M. / Jones, E.Y. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3. Authors: Zebisch, M. / Yvonne Jones, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ufs.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ufs.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ufs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ufs_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 4ufs_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 4ufs_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4ufs_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4ufs ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4ufs | HTTPS FTP |
-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: 54108.453 Da / Num. of mol.: 1 / 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.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: O75473 |
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#2: Protein | Mass: 13946.869 Da / Num. of mol.: 1 / Fragment: FU1-FU2, RESIDUES 39-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BFU0 |
#3: Protein | Mass: 18203.557 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 53-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) References: UniProt: Q5SSZ7, UniProt: Q9ULT6*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.61 Å3/Da / Density % sol: 73 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.100 M AMMONIUM ACETATE, 0.600 M SODIUM CHLORIDE, 0.050 M MES PH 6.0, 0.005 M MAGNESIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 4.8→40 Å / Num. obs: 7509 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 212 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 4.8→5.37 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 4.8→133.37 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R Free: 1.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROSMART RESTRAINTS APPLIED
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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: 256.386 Å2
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Refinement step | Cycle: LAST / Resolution: 4.8→133.37 Å
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