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- PDB-6d35: Crystal structure of Xenopus Smoothened in complex with cholesterol -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d35 | ||||||
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Title | Crystal structure of Xenopus Smoothened in complex with cholesterol | ||||||
![]() | Smoothened,Soluble cytochrome b562,Smoothened | ||||||
![]() | MEMBRANE PROTEIN / GPCR / Hedgehog signaling / Class Frizzled / Sterol | ||||||
Function / homology | ![]() tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / central nervous system development / G protein-coupled receptor activity / electron transport chain / cilium / membrane => GO:0016020 ...tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / central nervous system development / G protein-coupled receptor activity / electron transport chain / cilium / membrane => GO:0016020 / periplasmic space / electron transfer activity / iron ion binding / dendrite / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, P. / Zheng, S. / Kim, Y. / Kruse, A.C. / Salic, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.9 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 647.4 KB | Display | ![]() |
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Full document | ![]() | 651.2 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d32SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 67568.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: smo, Smo, cybC / Production host: ![]() ![]() References: UniProt: Q98SW5, UniProt: P0ABE7, UniProt: A0A1L8GTP2*PLUS |
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#2: Chemical | ChemComp-CLR / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.28 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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