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- PDB-4qin: Structure of the human smoothened receptor in complex with SAG1.5 -

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Basic information

Entry
Database: PDB / ID: 4qin
TitleStructure of the human smoothened receptor in complex with SAG1.5
ComponentsSmoothened homolog/Soluble cytochrome b562 chimeric protein
KeywordsSIGNALING PROTEIN / Human smoothened receptor / agonist / novel protein engineering / GPCR network / membrane protein / 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 / response to inositol / 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 ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / response to inositol / 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 / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / left/right axis specification / ciliary tip / Activation of SMO / patched binding / forebrain morphogenesis / type B pancreatic cell development / somite development / positive regulation of organ growth / dorsal/ventral neural tube patterning / BBSome-mediated cargo-targeting to cilium / smooth muscle tissue development / cellular response to cholesterol / thalamus development / positive regulation of branching involved in ureteric bud morphogenesis / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / pattern specification process / commissural neuron axon guidance / dopaminergic neuron differentiation / oxysterol binding / positive regulation of multicellular organism growth / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / neural crest cell migration / cAMP-dependent protein kinase inhibitor activity / cell fate specification / negative regulation of DNA binding / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / ciliary membrane / midgut development / hair follicle morphogenesis / smoothened signaling pathway / negative regulation of epithelial cell differentiation / positive regulation of neuroblast proliferation / protein kinase A catalytic subunit binding / heart looping / endoplasmic reticulum-Golgi intermediate compartment / odontogenesis of dentin-containing tooth / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / negative regulation of protein phosphorylation / skeletal muscle fiber development / homeostasis of number of cells within a tissue / centriole / protein sequestering activity / positive regulation of epithelial cell proliferation / epithelial cell proliferation / central nervous system development / astrocyte activation / electron transport chain / Hedgehog 'on' state / G protein-coupled receptor activity / multicellular organism growth / cerebral cortex development / cilium / positive regulation of protein import into nucleus / protein import into nucleus / osteoblast differentiation / 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 / 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
Chem-SG8 / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, 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)
CitationJournal: 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
DepositionMay 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)52,9212
Polymers52,3951
Non-polymers5261
Water1267
1
A: Smoothened homolog/Soluble cytochrome b562 chimeric protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)105,8424
Polymers104,7902
Non-polymers1,0522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2570 Å2
ΔGint-26 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.220, 158.930, 60.020
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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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-SG8 / 3-chloro-4,7-difluoro-N-[trans-4-(methylamino)cyclohexyl]-N-[3-(pyridin-4-yl)benzyl]-1-benzothiophene-2-carboxamide


Mass: 526.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26ClF2N3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 35

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100mM MgSO4, 100mM MES pH6.0, 30% PEG400, 2-3% Polypropylene glycol P 400, Lipidic Cubic Phase (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18991 / % possible obs: 87.5 % / Redundancy: 18.6 % / Biso Wilson estimate: 48.48 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 21.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.8 / % possible all: 53.6

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Two independent search models of SMO and BRIL domains from PDB entry 4JKV

4jkv


Resolution: 2.6→44.42 Å / Cor.coef. Fo:Fc: 0.8967 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 1.042 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE TRYPTOPHAN 365 SIDE CHAIN, WHICH POSSIBLY CAN BE A CHOLESTEROL. THIS HAS NOT BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 755 4.98 %RANDOM
Rwork0.2254 ---
obs0.2272 15154 72.11 %-
Displacement parametersBiso mean: 61.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.8374 Å20 Å2-0.8783 Å2
2--7.6523 Å20 Å2
3----6.8149 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 36 7 3454
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013542HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074837HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1546SINUSOIDAL6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes527HARMONIC5
X-RAY DIFFRACTIONt_it3542HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion2.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4566SEMIHARMONIC4
LS refinement shellResolution: 2.59→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3059 29 4.85 %
Rwork0.2574 569 -
all0.2597 598 -
obs--72.11 %

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