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- PDB-4c99: Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crysta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c99 | ||||||
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Title | Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crystal form I | ||||||
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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 | ![]() trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / frizzled binding / embryonic forelimb morphogenesis ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / frizzled binding / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / regulation of canonical Wnt signaling pathway / limb development / epithelial tube branching involved in lung morphogenesis / negative regulation of Wnt signaling pathway / bone mineralization / canonical Wnt signaling pathway / stem cell proliferation / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / osteoblast differentiation / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / heparin binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / signaling receptor binding / cell surface / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
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 | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 88.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c84C ![]() 4c85C ![]() 4c86C ![]() 4c8aC ![]() 4c8cC ![]() 4c8fC ![]() 4c8pC ![]() 4c8tC ![]() 4c8uC ![]() 4c8vC ![]() 4c8wC ![]() 4c9aC ![]() 4c9eC ![]() 4c9rC ![]() 4c9uC ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998, 0.042, -0.053), Vector: |
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Components
#1: Protein | Mass: 18203.557 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 53-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5SSZ7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 14158.086 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 37-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-CL / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.19 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→66 Å / Num. obs: 15525 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 71.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16 |
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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: 2.8→66.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.875 / SU B: 21.184 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→66.46 Å
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