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- PDB-4jkv: Structure of the human smoothened 7TM receptor in complex with an... -

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Basic information

Entry
Database: PDB / ID: 4jkv
TitleStructure of the human smoothened 7TM receptor in complex with an antitumor agent
ComponentsSoluble cytochrome b562, Smoothened homolog
KeywordsMEMBRANE 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 / 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 / positive regulation of branching involved in ureteric bud morphogenesis / cellular response to cholesterol / thalamus development / cerebellar cortex morphogenesis / pattern specification process / mammary gland epithelial cell differentiation / dentate gyrus development / 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) / cell fate specification / neural crest cell migration / cAMP-dependent protein kinase inhibitor activity / negative regulation of DNA binding / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / ciliary membrane / hair follicle morphogenesis / midgut development / negative regulation of epithelial cell differentiation / smoothened signaling pathway / positive regulation of neuroblast proliferation / endoplasmic reticulum-Golgi intermediate compartment / protein kinase A catalytic subunit binding / heart looping / odontogenesis of dentin-containing tooth / negative regulation of protein phosphorylation / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / homeostasis of number of cells within a tissue / centriole / protein sequestering activity / positive regulation of epithelial cell proliferation / central nervous system development / epithelial cell proliferation / astrocyte activation / electron transport chain / Hedgehog 'on' state / G protein-coupled receptor activity / multicellular organism growth / cerebral cortex development / positive regulation of protein import into nucleus / protein import into nucleus / osteoblast differentiation / endocytic vesicle membrane / late endosome / gene expression / in utero embryonic development / periplasmic space / electron transfer activity / protein stabilization / cilium / positive regulation of cell migration / iron ion binding / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / heme binding / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / 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. / Cytochrome c/b562 / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1KS / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.45 Å
AuthorsWang, 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)
CitationJournal: 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
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Nov 27, 2013Group: Structure summary
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Apr 3, 2024Group: 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 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562, Smoothened homolog
B: Soluble cytochrome b562, Smoothened homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,45416
Polymers106,2422
Non-polymers4,21214
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-14 kcal/mol
Surface area40840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.444, 98.177, 84.293
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Soluble cytochrome b562, Smoothened homolog / Cytochrome b-562 / SMO / Protein Gx


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 ChemComp-1KS / 4-fluoro-N-methyl-N-{1-[4-(1-methyl-1H-pyrazol-5-yl)phthalazin-1-yl]piperidin-4-yl}-2-(trifluoromethyl)benzamide


Mass: 512.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24F4N6O
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 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

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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: Dec 1, 2012 / 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: 2.45→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 shellResolution: 2.45→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
AutoSolphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 2202 5.03 %RANDOM
Rwork0.1997 ---
obs0.2013 43776 99.35 %-
Displacement parametersBiso mean: 74.42 Å2
Baniso -1Baniso -2Baniso -3
1-9.7708 Å20 Å21.3965 Å2
2---11.0598 Å20 Å2
3---1.289 Å2
Refine analyzeLuzzati coordinate error obs: 0.402 Å
Refinement stepCycle: LAST / Resolution: 2.45→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 237 110 7379
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097461HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9710113HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3371SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1084HARMONIC5
X-RAY DIFFRACTIONt_it7461HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion3.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion950SEMIHARMONIC5
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_contact9119SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2966 152 4.96 %
Rwork0.2352 2914 -
all0.2383 3066 -
obs--99.35 %
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)
11.2165-0.163-1.05032.61231.7992.7053-0.1593-0.2825-0.06090.1340.06460.03960.47760.26470.09470.00510.0209-0.07910.27080.0868-0.3585-11.23264.71843.8814
23.1075-0.38250.99880.6355-0.23831.0152-0.1032-0.49850.2460.15040.03320.11340.0315-0.25740.07-0.17780.00040.02360.0165-0.0964-0.1145-38.391119.814516.6583
31.23780.18320.04535.5830.79222.5364-0.02760.21310.1647-0.0621-0.0032-0.1619-0.02260.05230.0308-0.2185-0.02640.0330.08220.1289-0.10226.313432.6956-17.7637
42.69640.8357-0.31051.4472-0.02120.8969-0.17770.6152-0.1398-0.1490.12850.18060.0527-0.23770.0493-0.2549-0.03990.00430.0543-0.0581-0.1619-28.21078.0613-10.8824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-1 - A|106 }A-1 - 106
2X-RAY DIFFRACTION2{ A|190 - A|550 }A190 - 550
3X-RAY DIFFRACTION3{ B|0 - B|106 }B0 - 106
4X-RAY DIFFRACTION4{ B|190 - B|552 }B190 - 552

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