[English] 日本語
Yorodumi- PDB-4n4w: Structure of the human smoothened receptor in complex with SANT-1. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n4w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the human smoothened receptor in complex with SANT-1. | |||||||||
Components | Cytochrome b(562),Smoothened homolog | |||||||||
Keywords | Membrane Protein / Transport Protein / Human smoothened receptor / antitumor agent / novel protein engineering / GPCR network / PSI-Biology / Structural Genomics / GPCR / membrane | |||||||||
Function / homology | Function and homology information ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / negative regulation of hair follicle development / 9+0 non-motile cilium / central nervous system neuron differentiation / regulation of somatic stem cell population maintenance / pancreas morphogenesis / epithelial-mesenchymal cell signaling / : ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / negative regulation of hair follicle development / 9+0 non-motile cilium / central nervous system neuron differentiation / regulation of somatic stem cell population maintenance / pancreas morphogenesis / epithelial-mesenchymal cell signaling / : / myoblast migration / atrial septum morphogenesis / determination of left/right asymmetry in lateral mesoderm / contact inhibition / spinal cord dorsal/ventral patterning / left/right axis specification / ciliary tip / Activation of SMO / thalamus development / patched binding / somite development / positive regulation of branching involved in ureteric bud morphogenesis / type B pancreatic cell development / forebrain morphogenesis / dorsal/ventral neural tube patterning / cellular response to cholesterol / BBSome-mediated cargo-targeting to cilium / positive regulation of organ growth / smooth muscle tissue development / pattern specification process / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / positive regulation of multicellular organism growth / commissural neuron axon guidance / dopaminergic neuron differentiation / 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 / anterior/posterior pattern specification / ciliary membrane / positive regulation of mesenchymal cell proliferation / negative regulation of epithelial cell differentiation / smoothened signaling pathway / midgut development / 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 / neuroblast proliferation / endoplasmic reticulum-Golgi intermediate compartment / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / homeostasis of number of cells within a tissue / centriole / protein sequestering activity / negative regulation of protein phosphorylation / epithelial cell proliferation / central nervous system development / positive regulation of epithelial cell proliferation / G protein-coupled receptor activity / astrocyte activation / Hedgehog 'on' state / multicellular organism growth / cilium / cerebral cortex development / osteoblast differentiation / positive regulation of protein import into nucleus / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / in utero embryonic development / electron transfer activity / periplasmic space / protein stabilization / positive regulation of cell migration / iron ion binding / negative regulation of gene expression / intracellular membrane-bounded organelle / dendrite / apoptotic process / 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 | Shigella flexneri 5 str. 8401 (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Wang, C. / Wu, H. / Han, G.W. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR) | |||||||||
Citation | Journal: Nat Commun / Year: 2014 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4n4w.cif.gz | 202.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4n4w.ent.gz | 159.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n4w ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n4w | HTTPS FTP |
---|
-Related structure data
Related structure data | 4qimC 4qinC 4jkvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 53121.004 Da / Num. of mol.: 1 / Fragment: Residues 190-555 / Mutation: M29W, H124I, R128L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 5 str. 8401 (bacteria), (gene. exp.) Homo sapiens (human) Strain: 8401 / Gene: cybC, SFV_4255, SMO, SMOH / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q0SXH8, UniProt: Q99835 |
---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 15 molecules
#3: Chemical | ChemComp-SNT / ( | ||||||||
---|---|---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.9 Details: NH4F 150mM, HEPES PH 6.9 100mM, PEG 400 27%, Jeffamine 2.5%, Lipidic Cubic Phase (LCP), temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2012 / 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: 2.8→50 Å / Num. obs: 16010 / % possible obs: 94.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 77.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1526 / % possible all: 92.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JKV Resolution: 2.8→49.35 Å / Cor.coef. Fo:Fc: 0.9342 / Cor.coef. Fo:Fc free: 0.9077 / SU R Cruickshank DPI: 1.046 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.12 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.415 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.99 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|