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Yorodumi- PDB-4c9u: Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 cr... -
+Open data
-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 | ||||||
Components |
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Keywords | 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 | Function and homology information 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 / limb development / stem cell proliferation ...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 / 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 / heparin binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | XENOPUS TROPICALIS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å | ||||||
Authors | Zebisch, M. / Jones, E.Y. | ||||||
Citation | Journal: Nat.Commun. / Year: 2013 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c9u.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c9u.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c9u_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 4c9u_full_validation.pdf.gz | 458.2 KB | Display | |
Data in XML | 4c9u_validation.xml.gz | 21 KB | Display | |
Data in CIF | 4c9u_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9u ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9u | 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 (ref.) |
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Similar structure data |
-Links
-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.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog) Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) 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.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog) Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q5M7L6 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
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 |
-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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