[English] 日本語
Yorodumi- PDB-3n93: Crystal structure of human CRFR2 alpha extracellular domain in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n93 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 3 | |||||||||
Components |
| |||||||||
Keywords | Membrane protein / Hormone / Class B-GPCR / Extracellular domain / CRFR2 alpha extracellular domain / Neuropeptide / Selectivity | |||||||||
Function / homology | Function and homology information corticotropin-releasing hormone receptor binding / corticotropin-releasing hormone receptor 2 binding / positive regulation of membrane potential / varicosity / Class B/2 (Secretin family receptors) / response to corticosterone / detection of maltose stimulus / response to starvation / maltose transport complex / carbohydrate transport ...corticotropin-releasing hormone receptor binding / corticotropin-releasing hormone receptor 2 binding / positive regulation of membrane potential / varicosity / Class B/2 (Secretin family receptors) / response to corticosterone / detection of maltose stimulus / response to starvation / maltose transport complex / carbohydrate transport / response to immobilization stress / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to nutrient levels / response to glucose / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / axon terminus / digestion / hormone-mediated signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / hormone activity / outer membrane-bounded periplasmic space / cellular response to hypoxia / periplasmic space / DNA damage response / extracellular space / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Homo Sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Pal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E. | |||||||||
Citation | Journal: To be Published Title: Structural basis of ligand selectivity in human CRFR1 and CRFR2 alpha extracellular domain Authors: Pal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n93.cif.gz | 376.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n93.ent.gz | 309.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n93_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3n93_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3n93_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 3n93_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n93 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n93 | HTTPS FTP |
-Related structure data
Related structure data | 3n95C 3n96C 3c4mS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
|
-Components
#1: Protein | Mass: 53146.746 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRFR2 alpha / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS #2: Protein/peptide | | Mass: 1692.963 Da / Num. of mol.: 1 / Fragment: UNP residues 142-157 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: Q969E3 #3: Polysaccharide | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 9% PEG 4000 0.1M Sodium acetate 16% Glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 42571 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.125 / Net I/σ(I): 19.64 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C4M Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.406 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.14 Å2 / Biso mean: 38.404 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.489→2.554 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|