+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zaw | ||||||
---|---|---|---|---|---|---|---|
Title | GPC3-Unc5D octamer structure and role in cell migration | ||||||
![]() | Glypican-3 | ||||||
![]() | SIGNALING PROTEIN / Glycoprotein / Migration | ||||||
Function / homology | ![]() peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / : / regulation of protein localization to membrane / : / regulation of non-canonical Wnt signaling pathway / mesenchymal cell proliferation involved in ureteric bud development / Defective B3GALT6 causes EDSP2 and SEMDJL1 ...peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / : / regulation of protein localization to membrane / : / regulation of non-canonical Wnt signaling pathway / mesenchymal cell proliferation involved in ureteric bud development / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / cell proliferation involved in metanephros development / A tetrasaccharide linker sequence is required for GAG synthesis / negative regulation of peptidase activity / cell migration involved in gastrulation / HS-GAG biosynthesis / HS-GAG degradation / negative regulation of growth / positive regulation of Wnt signaling pathway, planar cell polarity pathway / coronary vasculature development / positive regulation of BMP signaling pathway / positive regulation of smoothened signaling pathway / regulation of canonical Wnt signaling pathway / embryonic hindlimb morphogenesis / 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 / anatomical structure morphogenesis / canonical Wnt signaling pathway / negative regulation of smoothened signaling pathway / Retinoid metabolism and transport / lysosomal lumen / osteoclast differentiation / epithelial cell proliferation / positive regulation of glucose import / Post-translational protein phosphorylation / response to bacterium / lung development / negative regulation of canonical Wnt signaling pathway / Golgi lumen / positive regulation of protein catabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / negative regulation of epithelial cell proliferation / positive regulation of canonical Wnt signaling pathway / cell migration / collagen-containing extracellular matrix / Attachment and Entry / endoplasmic reticulum lumen / 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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 192.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 127.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7za1C ![]() 7za2C ![]() 7za3C ![]() 7zavC ![]() 4ywtS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53383.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
---|---|---|---|
#2: Sugar | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris/BICINE (pH 8.5) and 0.02 M of amino acids (L-Na-glutamate, alanine, glycine, lysine-HCl, and serine) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→86.86 Å / Num. obs: 16895 / % possible obs: 100 % / Redundancy: 15.5 % / Biso Wilson estimate: 87.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.079 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.58→2.65 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1239 / CC1/2: 0.324 / Rpim(I) all: 1.39 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4YWT Resolution: 2.58→50.09 Å / SU ML: 0.5552 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.5576 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→50.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -19.0789262058 Å / Origin y: -23.9386677376 Å / Origin z: 11.8014785731 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |