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- PDB-4qim: Structure of the human smoothened receptor in complex with ANTA XV -

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Basic information

Entry
Database: PDB / ID: 4qim
TitleStructure of the human smoothened receptor in complex with ANTA XV
ComponentsSmoothened homolog/Soluble cytochrome b562 chimeric protein
KeywordsSIGNALING PROTEIN / Human smoothened receptor / antitumor agent / novel protein engineering / GPCR network / PSI-Biology / Structural Genomics / membrane protein / 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
Chem-A8T / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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

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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)52,9003
Polymers52,3951
Non-polymers5052
Water41423
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.830, 79.840, 170.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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-A8T / 2-{6-[4-(4-benzylphthalazin-1-yl)piperazin-1-yl]pyridin-3-yl}propan-2-ol


Mass: 439.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N5O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.2
Details: 100-115mM NH4Cl, 100mM HEPES pH7.2, 36% PEG400, 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: May 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: 17421 / % possible obs: 94.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 79.08 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 35
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 80.6

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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: 2.61→32.64 Å / Cor.coef. Fo:Fc: 0.9342 / Cor.coef. Fo:Fc free: 0.9173 / SU R Cruickshank DPI: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 901 5.19 %RANDOM
Rwork0.2234 ---
obs0.2255 17377 93.99 %-
Displacement parametersBiso mean: 97.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.8737 Å20 Å20 Å2
2---11.8447 Å20 Å2
3---13.7185 Å2
Refine analyzeLuzzati coordinate error obs: 0.466 Å
Refinement stepCycle: LAST / Resolution: 2.61→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 34 23 3576
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013650HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1622SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes539HARMONIC5
X-RAY DIFFRACTIONt_it3650HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion2.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4377SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.77 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3379 142 6.12 %
Rwork0.2205 2178 -
all0.2275 2320 -
obs--93.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92080.01390.27980.5652-0.54854.1131-0.13780.07050.0047-0.11880.0341-0.0329-0.1481-0.10850.1037-0.1493-0.1116-0.03330.11490.0823-0.305415.2152-10.5374-33.35
21.33631.54820.64378.74-0.51354.0699-0.0394-0.0094-0.0772-0.42730.0491-0.03180.35970.0143-0.0097-0.1036-0.16130.09880.099-0.0994-0.3589-14.0532-7.7742-84.2355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|190 - A|553 }A190 - 553
2X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

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