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- PDB-4o9r: Human Smoothened Receptor structure in complex with cyclopamine -

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Basic information

Entry
Database: PDB / ID: 4o9r
TitleHuman Smoothened Receptor structure in complex with cyclopamine
ComponentsSmoothened homolog/Soluble cytochrome b562 chimeric protein
KeywordsSIGNALING PROTEIN / serial femtosecond crystallography / human SMO receptor / cyclopamine / novel protein engineering / GPCR network / PSI-Biology / free electron laser / Structural Genomics / membrane protein / XFEL / LCP / room temperature structure / 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 / 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 ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / 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 / contact inhibition / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / left/right axis specification / ciliary tip / Activation of SMO / patched binding / thalamus development / somite development / type B pancreatic cell development / forebrain morphogenesis / cellular response to cholesterol / dorsal/ventral neural tube patterning / BBSome-mediated cargo-targeting to cilium / positive regulation of organ growth / positive regulation of branching involved in ureteric bud morphogenesis / 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 / centriole / protein sequestering activity / negative regulation of protein phosphorylation / epithelial cell proliferation / central nervous system development / electron transport chain / G protein-coupled receptor activity / positive regulation of epithelial cell proliferation / astrocyte activation / Hedgehog 'on' state / multicellular organism growth / cilium / cerebral cortex development / 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
Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain ...Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Cyclopamine / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.204 Å
AuthorsWang, C. / Weierstall, U. / James, D. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C.H. / Doak, R.B. / Nelson, G. / Fromme, P. ...Wang, C. / Weierstall, U. / James, D. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C.H. / Doak, R.B. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. / Liu, H. / Basu, S. / Wacker, D. / Han, G.W. / Katritch, V. / Boutet, S. / Messerschmidt, M. / Willams, G.J. / Koglin, J.E. / Seibert, M.M. / Klinker, M. / Gati, C. / Shoeman, R.L. / Barty, A. / Chapman, H.N. / Kirian, R.A. / Beyerlein, K.R. / Stevens, R.C. / Li, D. / Shah, S.T.A. / Howe, N. / Caffrey, M. / Cherezov, V. / GPCR Network (GPCR)
CitationJournal: Nat Commun / Year: 2014
Title: Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.
Authors: Weierstall, U. / James, D. / Wang, C. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C. / Bruce Doak, R. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. ...Authors: Weierstall, U. / James, D. / Wang, C. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C. / Bruce Doak, R. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. / Liu, H. / Basu, S. / Wacker, D. / Han, G.W. / Katritch, V. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Koglin, J.E. / Marvin Seibert, M. / Klinker, M. / Gati, C. / Shoeman, R.L. / Barty, A. / Chapman, H.N. / Kirian, R.A. / Beyerlein, K.R. / Stevens, R.C. / Li, D. / Shah, S.T. / Howe, N. / Caffrey, M. / Cherezov, V.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Smoothened homolog/Soluble cytochrome b562 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8072
Polymers52,3951
Non-polymers4121
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 157.300, 52.400
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Smoothened homolog/Soluble cytochrome b562 chimeric 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.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q99835, UniProt: P0ABE7
#2: Chemical ChemComp-CY8 / Cyclopamine / (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol / Cyclopamine


Mass: 411.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41NO2 / Comment: alkaloid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 100 mM Hepes, 30 % (v/v) PEG 400, 100 mM NaCl , pH 7.0, Lipidic Cubic Phase (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 1, 2013
RadiationMonochromator: K-B Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 10785 / % possible obs: 100 %
Reflection shellResolution: 3.2→3.7 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JKV for SMO and PDB ENTRY 4IB4 for BRIL

4jkv

4ib4


Resolution: 3.204→39.325 Å / SU ML: 0.5 / σ(F): 1.38 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 399 4.94 %
Rwork0.2317 --
obs0.2339 8082 75.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.204→39.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 30 0 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033513
X-RAY DIFFRACTIONf_angle_d0.6134807
X-RAY DIFFRACTIONf_dihedral_angle_d11.9271183
X-RAY DIFFRACTIONf_chiral_restr0.024553
X-RAY DIFFRACTIONf_plane_restr0.003603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2041-3.66750.4084630.3491137X-RAY DIFFRACTION33
3.6675-4.61950.3241520.25823133X-RAY DIFFRACTION93
4.6195-39.32790.24131840.2033413X-RAY DIFFRACTION100

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