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- PDB-2mah: Solution structure of Smoothened -

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Basic information

Entry
Database: PDB / ID: 2mah
TitleSolution structure of Smoothened
ComponentsProtein smoothened
KeywordsONCOPROTEIN / Smoothened / Hedgehog
Function / homology
Function and homology information


Activation of SMO / blastoderm segmentation / 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 ...Activation of SMO / blastoderm segmentation / 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 / 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 / somatic stem cell population maintenance / regulation of mitotic cell cycle / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / central nervous system development / G protein-coupled receptor activity / positive regulation of protein localization to plasma membrane / cilium / regulation of apoptotic process / neuronal cell body / dendrite / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Frizzled cysteine-rich domain / Frizzled cysteine-rich 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 / Frizzled cysteine-rich 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRana, R. / Lee, H. / Zheng, J.J.
CitationJournal: Nat Commun / Year: 2013
Title: Structural insights into the role of the Smoothened cysteine-rich domain in Hedgehog signalling.
Authors: Rana, R. / Carroll, C.E. / Lee, H.J. / Bao, J. / Marada, S. / Grace, C.R. / Guibao, C.D. / Ogden, S.K. / Zheng, J.J.
History
DepositionJul 9, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein smoothened


Theoretical massNumber of molelcules
Total (without water)14,8811
Polymers14,8811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein smoothened / SMOH / Smooth / dSMO


Mass: 14881.296 Da / Num. of mol.: 1 / Fragment: FZ domain (UNP residues 85-202)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: smo, CG11561 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P91682

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HBHA(CO)NH
1713D 1H-15N NOESY

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Sample preparation

DetailsContents: 200 uM protein, 10 mM [U-2H] acetic acid, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMprotein-11
10 mMacetic acid-2[U-2H]1
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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