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Open data
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Basic information
Entry | Database: PDB / ID: 6o3a | ||||||
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Title | Crystal structure of Frizzled 7 CRD in complex with F7.B Fab | ||||||
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![]() | SIGNALING PROTEIN / Receptor / Wnt / Frizzled / CRD / Antibody | ||||||
Function / homology | ![]() negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / non-canonical Wnt signaling pathway / Wnt receptor activity / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping / Wnt-protein binding ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / non-canonical Wnt signaling pathway / Wnt receptor activity / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping / Wnt-protein binding / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / regulation of canonical Wnt signaling pathway / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of phosphorylation / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / positive regulation of JNK cascade / neuron differentiation / recycling endosome membrane / T cell differentiation in thymus / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raman, S. / Beilschmidt, M. / Fransson, J. / Julien, J.P. | ||||||
![]() | ![]() Title: Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies. Authors: Raman, S. / Beilschmidt, M. / To, M. / Lin, K. / Lui, F. / Jmeian, Y. / Ng, M. / Fernandez, M. / Fu, Y. / Mascall, K. / Duque, A. / Wang, X. / Pan, G. / Angers, S. / Moffat, J. / Sidhu, S.S. ...Authors: Raman, S. / Beilschmidt, M. / To, M. / Lin, K. / Lui, F. / Jmeian, Y. / Ng, M. / Fernandez, M. / Fu, Y. / Mascall, K. / Duque, A. / Wang, X. / Pan, G. / Angers, S. / Moffat, J. / Sidhu, S.S. / Magram, J. / Sinclair, A.M. / Fransson, J. / Julien, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.5 KB | Display | ![]() |
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PDB format | ![]() | 97.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.2 KB | Display | ![]() |
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Full document | ![]() | 490.9 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o39C ![]() 6o3bC ![]() 5bpqS S: Starting model for refinement 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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Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23209.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23404.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 3 molecules E![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein | Mass: 15057.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#7: Sugar |
-Non-polymers , 4 types, 315 molecules ![](data/chem/img/CXS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CXS / | ||||
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#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 10 Details: 0.1 M CAPS, pH 10.5, 20% (w/v) PEG 3350, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.551 Å / Num. obs: 37237 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 1.12 / CC1/2: 0.701 / Rpim(I) all: 0.438 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5bpq Resolution: 2.1→38.551 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.551 Å
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Refine LS restraints |
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LS refinement shell |
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