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Open data
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Basic information
Entry | Database: PDB / ID: 7za2 | ||||||
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Title | GPC3-Unc5D octamer structure and role in cell migration | ||||||
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![]() | SIGNALING PROTEIN / Complex / Cell migration / Glycan-Glycan Interaction | ||||||
Function / homology | ![]() 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 / netrin receptor activity / regulation of non-canonical Wnt signaling pathway ...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 / netrin receptor activity / regulation of non-canonical Wnt signaling pathway / mesenchymal cell proliferation involved in ureteric bud development / Retinoid metabolism and transport / 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 / regulation of neuron migration / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cell-cell adhesion via plasma-membrane adhesion molecules / coronary vasculature development / pyramidal neuron differentiation / positive regulation of BMP signaling pathway / 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 / branching involved in ureteric bud morphogenesis / smoothened signaling pathway / bone mineralization / positive regulation of endocytosis / canonical Wnt signaling pathway / side of membrane / negative regulation of smoothened signaling pathway / osteoclast differentiation / epithelial cell proliferation / kidney development / axon guidance / positive regulation of glucose import / animal organ morphogenesis / response to bacterium / lung development / negative regulation of canonical Wnt signaling pathway / Golgi lumen / positive regulation of protein catabolic process / negative regulation of epithelial cell proliferation / positive regulation of canonical Wnt signaling pathway / cell migration / collagen-containing extracellular matrix / lysosome / negative regulation of cell population proliferation / apoptotic process / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7za1C ![]() 7za3C ![]() 7zavC ![]() 7zawC ![]() 5fttS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53323.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 30257.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 8.5 Details: 15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine ...Details: 15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine HCL, trans-4-hydroxyl-L-proline). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→66.62 Å / Num. obs: 21870 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 245.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09281 / Rpim(I) all: 0.03962 / Net I/σ(I): 7.77 |
Reflection shell | Resolution: 4.6→4.76 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2165 / CC1/2: 0.485 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FTT, GPC3 Resolution: 4.6→66.616 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.891 / SU B: 486.107 / SU ML: 2.381 / Cross valid method: FREE R-VALUE / ESU R Free: 1.626 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 331.565 Å2
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Refinement step | Cycle: LAST / Resolution: 4.6→66.616 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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