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- PDB-5v56: 2.9A XFEL structure of the multi-domain human smoothened receptor... -
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Basic information
Entry | Database: PDB / ID: 5v56 | ||||||
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Title | 2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114 | ||||||
![]() | Smoothened homolog,Flavodoxin,Smoothened homolog | ||||||
![]() | MEMBRANE PROTEIN / human smoothened receptor complex / GPCR Hedgehog signaling / GPCR / Class F / 7TM domain / hinge domain / extracellular cystein-rich domain / Flavodoxin / LCP / XFEL / TC114 | ||||||
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 / 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 / FMN binding / gene expression / in utero embryonic development / electron transfer activity / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / dendrite / 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 | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. ...Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F. | ||||||
![]() | ![]() Title: Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / ...Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 260.2 KB | Display | ![]() |
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PDB format | ![]() | 205.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v57C ![]() 1i1oS ![]() 4c79S ![]() 4qimS C: citing same article ( S: Starting model for refinement |
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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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
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Components
#1: Protein | Mass: 72576.586 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 53-433,444-558 / Mutation: E194E, P2A, Y98W Source method: isolated from a genetically manipulated source Details: The fusion protein of Smoothened homolog (RESIDUES 53-433), Flavodoxin (RESIDUES 1002-1148), Smoothened homolog (RESIDUES 444-558) and 10 HIS tags Source: (gene. exp.) ![]() ![]() Gene: SMO, SMOH, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Production host: ![]() #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG400, 50-200 mM Ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 4, 2016 / Details: K-B mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→24.9 Å / Num. obs: 37101 / % possible obs: 100 % / Redundancy: 366 % / Biso Wilson estimate: 82.2 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 64.5 % / Rmerge(I) obs: 2.8 / Mean I/σ(I) obs: 0.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C79, 4QIM, 1I1O Resolution: 2.9→24.9 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.886 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.34
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Displacement parameters | Biso mean: 117.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→24.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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