[English] 日本語
Yorodumi- PDB-5ii0: Crystal structure of the human calcitonin receptor ectodomain in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ii0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human calcitonin receptor ectodomain in complex with a truncated salmon calcitonin analogue | ||||||
Components |
| ||||||
Keywords | HORMONE / calcitonin / G protein coupled receptor / peptide hormone / ectodomain | ||||||
Function / homology | Function and homology information calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity ...calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity / Calcitonin-like ligand receptors / negative regulation of ossification / positive regulation of protein kinase A signaling / response to amyloid-beta / ossification / response to glucocorticoid / regulation of mRNA stability / positive regulation of calcium-mediated signaling / osteoclast differentiation / acrosomal vesicle / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / cilium / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / axon / positive regulation of gene expression / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oncorhynchus gorbuscha (pink salmon) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.097 Å | ||||||
Authors | Johansson, E. / Reedtz-Runge, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Type II Turn of Receptor-bound Salmon Calcitonin Revealed by X-ray Crystallography. Authors: Johansson, E. / Hansen, J.L. / Hansen, A.M. / Shaw, A.C. / Becker, P. / Schaffer, L. / Reedtz-Runge, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ii0.cif.gz | 166 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ii0.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ii0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ii0_validation.pdf.gz | 482.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ii0_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 5ii0_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 5ii0_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5ii0 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5ii0 | HTTPS FTP |
-Related structure data
Related structure data | 3n7sS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14433.183 Da / Num. of mol.: 3 / Fragment: ectodomain UNP residues 25-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALCR / Variant: isoform II / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30988 #2: Protein/peptide | Mass: 2791.992 Da / Num. of mol.: 3 / Fragment: UNP residues 8-32 / Source method: obtained synthetically / Source: (synth.) Oncorhynchus gorbuscha (pink salmon) / References: UniProt: Q8QG84, UniProt: Q91970*PLUS #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-URE / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes, pH 7.5, 4.3 M sodium chloride, 2 M urea |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.097→24.84 Å / Num. obs: 31627 / % possible obs: 97 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.59 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.99 |
Reflection shell | Resolution: 2.097→2.172 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.86 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N7S Resolution: 2.097→24.84 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 21.45
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.097→24.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 29.6999 Å / Origin y: 1.4964 Å / Origin z: -1.6102 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |