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- PDB-8oij: Drosophila Smaug-Smoothened complex -

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Basic information

Entry
Database: PDB / ID: 8oij
TitleDrosophila Smaug-Smoothened complex
Components
  • Protein Smaug
  • Protein smoothened
KeywordsRNA BINDING PROTEIN / translation repressor / Hedgehog signaling
Function / homology
Function and homology information


Activation of SMO / blastoderm segmentation / establishment of RNA localization / Activation of CI / Activation of SMO / Hedgehog 'off' state / Bolwig's organ morphogenesis / Phosphorylation of SMO / eye-antennal disc morphogenesis / Assembly of the 'signalling complexes' ...Activation of SMO / blastoderm segmentation / establishment of RNA localization / Activation of CI / Activation of SMO / Hedgehog 'off' state / Bolwig's organ morphogenesis / Phosphorylation of SMO / eye-antennal disc morphogenesis / Assembly of the 'signalling complexes' / anterior/posterior lineage restriction, imaginal disc / compound eye morphogenesis / follicle cell of egg chamber development / wing disc anterior/posterior pattern formation / mucosal immune response / segment polarity determination / imaginal disc-derived wing morphogenesis / nuclear-transcribed mRNA poly(A) tail shortening / patched binding / pattern specification process / regulation of stem cell differentiation / commissural neuron axon guidance / phosphatidylinositol-4-phosphate binding / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / myosin binding / somatic stem cell population maintenance / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / translation repressor activity / regulation of mitotic cell cycle / regulation of mRNA stability / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / mRNA regulatory element binding translation repressor activity / central nervous system development / mRNA 3'-UTR binding / G protein-coupled receptor activity / positive regulation of protein localization to plasma membrane / P-body / cilium / regulation of apoptotic process / negative regulation of translation / mRNA binding / neuronal cell body / dendrite / positive regulation of gene expression / regulation of DNA-templated transcription / protein kinase binding / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Smaug, PHAT analogous topology / PHAT / Smaug, PHAT domain superfamily / Protein Smaug, SAM 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 ...Smaug, PHAT analogous topology / PHAT / Smaug, PHAT domain superfamily / Protein Smaug, SAM 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. / SAM domain (Sterile alpha motif) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein smoothened / Protein Smaug
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUbartaite, G. / Kubikova, J. / Jeske, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar.
Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M.
#1: Journal: bioRxiv / Year: 2023
Title: Structural basis for binding of Smaug to the GPCR Smoothened and to the germline inducer Oskar
Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Smaug
B: Protein Smaug
C: Protein smoothened
D: Protein smoothened
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7927
Polymers47,5624
Non-polymers2303
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-80 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.590, 76.590, 268.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-440-

HOH

21B-444-

HOH

31B-447-

HOH

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Components

#1: Protein Protein Smaug


Mass: 19964.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Although the construct is a fusion, we don't know which Smo peptide is finally bound to which Smaug binding pocket. The linker is long enough that both scenarios are possible.,Although the ...Details: Although the construct is a fusion, we don't know which Smo peptide is finally bound to which Smaug binding pocket. The linker is long enough that both scenarios are possible.,Although the construct is a fusion, we don't know which Smo peptide is finally bound to which Smaug binding pocket. The linker is long enough that both scenarios are possible.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: smg, CG5263 / Production host: Escherichia coli (E. coli) / References: UniProt: Q23972
#2: Protein/peptide Protein smoothened / dSMO / SMOH / Smooth


Mass: 3816.067 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Although the construct is a fusion, we don't know which Smo peptide is finally bound to which Smaug binding pocket. The linker is long enough that both scenarios are possible.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: smo, CG11561 / Production host: Escherichia coli (E. coli) / References: UniProt: P91682
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 5 % (w/v) PEG 3000, 20 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2→66.33 Å / Num. obs: 21810 / % possible obs: 94 % / Redundancy: 9.9 % / Biso Wilson estimate: 38.62 Å2 / CC1/2: 0.996 / Net I/σ(I): 7
Reflection shellResolution: 2→2.23 Å / Num. unique obs: 1090 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.39 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.9412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2925 1998 9.17 %
Rwork0.2719 19789 -
obs0.2737 21787 66.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.48 Å2
Refinement stepCycle: LAST / Resolution: 2→64.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 15 94 2924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182873
X-RAY DIFFRACTIONf_angle_d1.52793904
X-RAY DIFFRACTIONf_chiral_restr0.0944475
X-RAY DIFFRACTIONf_plane_restr0.0045491
X-RAY DIFFRACTIONf_dihedral_angle_d18.41072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.998550.932655X-RAY DIFFRACTION2.67
2.05-2.110.6127160.5089154X-RAY DIFFRACTION7.55
2.11-2.170.3856340.3806327X-RAY DIFFRACTION15.87
2.17-2.240.3095540.3461535X-RAY DIFFRACTION25.95
2.24-2.320.2806680.341687X-RAY DIFFRACTION32.93
2.32-2.410.31131130.35171116X-RAY DIFFRACTION53.88
2.41-2.520.33751790.33241775X-RAY DIFFRACTION85.55
2.52-2.650.3662120.32862104X-RAY DIFFRACTION99.74
2.65-2.820.33932120.32272099X-RAY DIFFRACTION99.91
2.82-3.040.30622120.29092106X-RAY DIFFRACTION99.78
3.04-3.340.28442160.28762126X-RAY DIFFRACTION99.87
3.34-3.830.27142170.25572158X-RAY DIFFRACTION99.92
3.83-4.820.24532210.22892190X-RAY DIFFRACTION99.83
4.82-64.390.30292390.25072357X-RAY DIFFRACTION99.73

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