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- PDB-4c9u: Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 cr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c9u | ||||||
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Title | Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II | ||||||
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![]() | LIGASE/SIGNALING PROTEIN / LIGASE-SIGNALING PROTEIN COMPLEX / WNT / RNF43 / LGR4 / LGR5 / LGR6 / RSPO / R-SPONDIN / R-SPO / RSPO1 / RSPO3 / RSPO4 / RECEPTOR / MEMBRANE / SIGNALLING | ||||||
Function / homology | ![]() anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / frizzled binding / limb development ...anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / frizzled binding / limb development / stem cell proliferation / skeletal system development / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heparin binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | XENOPUS TROPICALIS | ||||||
Method | ![]() ![]() | ||||||
![]() | Zebisch, M. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin. Authors: Zebisch, M. / Xu, Y. / Krastev, C. / Macdonald, B.T. / Chen, M. / Gilbert, R.J.C. / He, X. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 453.7 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c84C ![]() 4c85C ![]() 4c86C ![]() 4c8aC ![]() 4c8cC ![]() 4c8fC ![]() 4c8pC ![]() 4c8tC ![]() 4c8uC ![]() 4c8vC ![]() 4c8wC ![]() 4c99C ![]() 4c9aC ![]() 4c9eC ![]() 4c9rC ![]() 4c9vC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20494.014 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 24-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: ![]() References: UniProt: Q08D68, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 13781.749 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 35-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3→52.23 Å / Num. obs: 13655 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.2 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3→50.5 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.842 / SU B: 22.711 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOCAL NCS RESTRAINTS HAVE BEEN USED
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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: 67.23 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50.5 Å
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Refine LS restraints |
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