+Open data
-Basic information
Entry | Database: PDB / ID: 7zav | ||||||
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Title | GPC3-Unc5D octamer structure and role in cell migration | ||||||
Components | Glypican-3 | ||||||
Keywords | SIGNALING PROTEIN / Glycoprotein / Migration | ||||||
Function / homology | Function and homology information peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / body morphogenesis / cell proliferation involved in kidney development / regulation of protein localization to membrane / regulation of non-canonical Wnt signaling pathway / Retinoid metabolism and transport ...peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / body morphogenesis / cell proliferation involved in kidney development / regulation of protein localization to membrane / regulation of non-canonical Wnt signaling pathway / Retinoid metabolism and transport / mesenchymal cell proliferation involved in ureteric bud development / cell proliferation involved in metanephros development / cell migration involved in gastrulation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of growth / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of BMP signaling pathway / coronary vasculature development / positive regulation of smoothened signaling pathway / embryonic hindlimb morphogenesis / regulation of canonical Wnt signaling pathway / regulation of growth / Wnt signaling pathway, planar cell polarity pathway / anterior/posterior axis specification / smoothened signaling pathway / branching involved in ureteric bud morphogenesis / bone mineralization / positive regulation of endocytosis / canonical Wnt signaling pathway / negative regulation of smoothened signaling pathway / side of membrane / osteoclast differentiation / epithelial cell proliferation / kidney development / positive regulation of glucose import / response to bacterium / animal organ morphogenesis / lung development / negative regulation of canonical Wnt signaling pathway / Golgi lumen / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / negative regulation of epithelial cell proliferation / cell migration / collagen-containing extracellular matrix / lysosome / negative regulation of cell population proliferation / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Ritu, R. / Agirre, J. ...Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Ritu, R. / Agirre, J. / Aksu, M. / White, E. / Lowe, E. / Ben Amar, D. / Zaballa, S. / Huo, J. / Pakos, I. / McCubbin, P. / Comoletti, D. / Owens, R. / Robinson, C. / Castellani, V. / del Toro, D. / Seiradake, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell / Year: 2022 Title: GPC3-Unc5 receptor complex structure and role in cell migration. Authors: Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero-Ordaz, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Raj, R. / Agirre, J. / Aksu, M. / White, E.S. ...Authors: Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero-Ordaz, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Raj, R. / Agirre, J. / Aksu, M. / White, E.S. / Lowe, E. / Ben Amar, D. / Zaballa, S. / Huo, J. / Pakos, I. / McCubbin, P.T.N. / Comoletti, D. / Owens, R.J. / Robinson, C.V. / Castellani, V. / Del Toro, D. / Seiradake, E. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zav.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zav.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/7zav ftp://data.pdbj.org/pub/pdb/validation_reports/za/7zav | HTTPS FTP |
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-Related structure data
Related structure data | 7za1C 7za2C 7za3C 7zawC 4ywtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53323.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpc3 / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q8CFZ4 | ||
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#2: Sugar | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate and 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→90.76 Å / Num. obs: 12106 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 92.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.065 / Rrim(I) all: 0.143 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 875 / CC1/2: 0.493 / Rpim(I) all: 0.999 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YWT Resolution: 2.9→43.94 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / Phase error: 31.8973 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.61 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→43.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.4804829562 Å / Origin y: -24.6206763277 Å / Origin z: 12.1716553409 Å
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Refinement TLS group | Selection details: all |