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- PDB-4qim: Structure of the human smoothened receptor in complex with ANTA XV -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qim | ||||||
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Title | Structure of the human smoothened receptor in complex with ANTA XV | ||||||
![]() | Smoothened homolog/Soluble cytochrome b562 chimeric protein | ||||||
![]() | SIGNALING PROTEIN / Human smoothened receptor / antitumor agent / novel protein engineering / GPCR network / PSI-Biology / Structural Genomics / membrane protein / GPCR / membrane | ||||||
Function / homology | ![]() ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / central nervous system neuron differentiation / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / central nervous system neuron differentiation / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling / myoblast migration / atrial septum morphogenesis / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / left/right axis specification / ciliary tip / Activation of SMO / thalamus development / somite development / patched binding / forebrain morphogenesis / cellular response to cholesterol / type B pancreatic cell development / dorsal/ventral neural tube patterning / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of organ growth / BBSome-mediated cargo-targeting to cilium / smooth muscle tissue development / pattern specification process / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / positive regulation of multicellular organism growth / dopaminergic neuron differentiation / commissural neuron axon guidance / oxysterol binding / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / cell fate specification / neural crest cell migration / cAMP-dependent protein kinase inhibitor activity / ciliary membrane / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / negative regulation of epithelial cell differentiation / midgut development / smoothened signaling pathway / hair follicle morphogenesis / positive regulation of neuroblast proliferation / heart looping / negative regulation of DNA binding / odontogenesis of dentin-containing tooth / protein kinase A catalytic subunit binding / endoplasmic reticulum-Golgi intermediate compartment / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / homeostasis of number of cells within a tissue / protein sequestering activity / centriole / negative regulation of protein phosphorylation / epithelial cell proliferation / central nervous system development / positive regulation of epithelial cell proliferation / astrocyte activation / G protein-coupled receptor activity / electron transport chain / Hedgehog 'on' state / multicellular organism growth / cerebral cortex development / cilium / positive regulation of protein import into nucleus / osteoblast differentiation / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / in utero embryonic development / periplasmic space / electron transfer activity / protein stabilization / positive regulation of cell migration / iron ion binding / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / dendrite / heme binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C. / Wu, H. / Evron, T. / Vardy, E. / Han, G.W. / Huang, X.-P. / Hufeisen, S.J. / Mangano, T.J. / Urban, D.J. / Katritch, V. ...Wang, C. / Wu, H. / Evron, T. / Vardy, E. / Han, G.W. / Huang, X.-P. / Hufeisen, S.J. / Mangano, T.J. / Urban, D.J. / Katritch, V. / Cherezov, V. / Caron, M.G. / Roth, B.L. / Stevens, R.C. / GPCR Network (GPCR) | ||||||
![]() | ![]() Title: Structural basis for Smoothened receptor modulation and chemoresistance to anticancer drugs. Authors: Wang, C. / Wu, H. / Evron, T. / Vardy, E. / Han, G.W. / Huang, X.P. / Hufeisen, S.J. / Mangano, T.J. / Urban, D.J. / Katritch, V. / Cherezov, V. / Caron, M.G. / Roth, B.L. / Stevens, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.2 KB | Display | ![]() |
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PDB format | ![]() | 155.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 692.6 KB | Display | ![]() |
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Full document | ![]() | 698 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n4wC ![]() 4qinC ![]() 4jkvS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
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Components
#1: Protein | Mass: 52395.199 Da / Num. of mol.: 1 Fragment: UNP Q99835 residues 190-433, P0ABE7 residues 23-128, Q99835 residues 441-555 Mutation: M1007W, H1102I, R1106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pFASTBAC / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-A8T / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.2 Details: 100-115mM NH4Cl, 100mM HEPES pH7.2, 36% PEG400, Lipidic Cubic Phase (LCP), temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 1, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 17421 / % possible obs: 94.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 79.08 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 80.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Two independent search models of SMO and BRIL domains from PDB entry 4JKV Resolution: 2.61→32.64 Å / Cor.coef. Fo:Fc: 0.9342 / Cor.coef. Fo:Fc free: 0.9173 / SU R Cruickshank DPI: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 97.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.466 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→32.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.77 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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