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Yorodumi- PDB-4jkv: Structure of the human smoothened 7TM receptor in complex with an... -
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-Basic information
Entry | Database: PDB / ID: 4jkv | ||||||
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Title | Structure of the human smoothened 7TM receptor in complex with an antitumor agent | ||||||
Components | Soluble cytochrome b562, Smoothened homolog | ||||||
Keywords | MEMBRANE 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 | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.45 Å | ||||||
Authors | Wang, C. / Wu, H. / Katritch, V. / Han, G.W. / Huang, X. / Liu, W. / Siu, F.Y. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR) | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structure of the human smoothened receptor bound to an antitumour agent. Authors: Wang, C. / Wu, H. / Katritch, V. / Han, G.W. / Huang, X.P. / Liu, W. / Siu, F.Y. / Roth, B.L. / Cherezov, V. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jkv.cif.gz | 373.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jkv.ent.gz | 304.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/4jkv ftp://data.pdbj.org/pub/pdb/validation_reports/jk/4jkv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53121.004 Da / Num. of mol.: 2 / Fragment: BRIL / Mutation: M7W, H101I, R107L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, SMO_HUMAN, SMO, SMOH / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: Q99835 |
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-Non-polymers , 7 types, 124 molecules
#2: Chemical | #3: Chemical | ChemComp-OLC / ( #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.8 Details: 100 mM HEPES, pH 7.8, 70 mM ammonium fluoride, 32% (v/v) PEG400, 4% 8% (v/v) P400, Lipidic Cubic Phase (LCP), temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 2.45→50 Å / Num. obs: 43797 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 63.52 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: Experimental Phasing by using Ta6Br12 soak Resolution: 2.45→42.12 Å / Cor.coef. Fo:Fc: 0.9432 / Cor.coef. Fo:Fc free: 0.9285 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 74.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.402 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→42.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Total num. of bins used: 20
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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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