[English] 日本語
Yorodumi- PDB-6d35: Crystal structure of Xenopus Smoothened in complex with cholesterol -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d35 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Xenopus Smoothened in complex with cholesterol | ||||||
Components | Smoothened,Soluble cytochrome b562,Smoothened | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / Hedgehog signaling / Class Frizzled / Sterol | ||||||
Function / homology | Function and homology information tissue development / smoothened signaling pathway / electron transport chain / G protein-coupled receptor activity / cilium / Wnt signaling pathway / membrane => GO:0016020 / periplasmic space / electron transfer activity / iron ion binding ...tissue development / smoothened signaling pathway / electron transport chain / G protein-coupled receptor activity / cilium / Wnt signaling pathway / membrane => GO:0016020 / periplasmic space / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Huang, P. / Zheng, S. / Kim, Y. / Kruse, A.C. / Salic, A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Cell / Year: 2018 Title: Structural Basis of Smoothened Activation in Hedgehog Signaling. Authors: Huang, P. / Zheng, S. / Wierbowski, B.M. / Kim, Y. / Nedelcu, D. / Aravena, L. / Liu, J. / Kruse, A.C. / Salic, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d35.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d35.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 6d35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/6d35 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/6d35 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6d32SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 67568.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog), (gene. exp.) Escherichia coli (E. coli) Gene: smo, Smo, cybC / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q98SW5, UniProt: P0ABE7, UniProt: A0A1L8GTP2*PLUS |
---|---|
#2: Chemical | ChemComp-CLR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 35-45% PEG 300, 300-500 mM LiSO4, 0.1 M MES pH 6-6.5 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0333 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.9→50 Å / Num. obs: 8172 / % possible obs: 79.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 81.04 Å2 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.139 / Rrim(I) all: 0.239 / Χ2: 1.495 / Net I/σ(I): 5 / Num. measured all: 18197 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D32 Resolution: 3.9→36.098 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.62 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.78 Å2 / Biso mean: 82.509 Å2 / Biso min: 25.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.9→36.098 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
|