+Open data
-Basic information
Entry | Database: PDB / ID: 7sz8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human CELSR1 EC4-7 | |||||||||
Components | Cadherin EGF LAG seven-pass G-type receptor 1 | |||||||||
Keywords | CELL ADHESION / planar cell polarity / signaling / Cadherin EGF LAG seven-pass G-type receptor 1 | |||||||||
Function / homology | Function and homology information orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / protein localization involved in establishment of planar polarity / establishment of body hair planar orientation / establishment of planar polarity of embryonic epithelium / establishment of planar polarity / apical protein localization / Wnt signaling pathway, planar cell polarity pathway / homophilic cell adhesion via plasma membrane adhesion molecules ...orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / protein localization involved in establishment of planar polarity / establishment of body hair planar orientation / establishment of planar polarity of embryonic epithelium / establishment of planar polarity / apical protein localization / Wnt signaling pathway, planar cell polarity pathway / homophilic cell adhesion via plasma membrane adhesion molecules / Rho protein signal transduction / central nervous system development / neural tube closure / G protein-coupled receptor activity / regulation of actin cytoskeleton organization / cell-cell adhesion / neuron migration / membrane => GO:0016020 / calcium ion binding / nucleoplasm / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.337 Å | |||||||||
Authors | Tamilselvan, E. / Sotomayor, M. | |||||||||
Funding support | 1items
| |||||||||
Citation | Journal: to be published Title: Crystal structure of human CELSR1 EC4-7 Authors: Tamilselvan, E. / Sotomayor, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7sz8.cif.gz | 321.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7sz8.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 7sz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sz8_validation.pdf.gz | 6.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7sz8_full_validation.pdf.gz | 6.9 MB | Display | |
Data in XML | 7sz8_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 7sz8_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/7sz8 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/7sz8 | HTTPS FTP |
-Related structure data
Related structure data | 5sznS 5t9tS 5v5xS 6c13S 6e6bS 6vg4S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49165.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CELSR1, CDHF9, FMI2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q9NYQ6 |
---|
-Non-polymers , 5 types, 177 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M magnesium chloride, 0.1 M MES pH 7.3, 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.337→46.378 Å / Num. obs: 47823 / % possible obs: 85.3 % / Redundancy: 3.3 % / CC1/2: 0.992 / Net I/σ(I): 15.375 |
Reflection shell | Resolution: 2.337→2.39 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 8.824 / Num. unique obs: 1953 / CC1/2: 0.984 / % possible all: 82.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4 Resolution: 2.337→46.378 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 16.6 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.396 / ESU R Free: 0.291 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 37.087 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.337→46.378 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|