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- PDB-6d32: Crystal structure of Xenopus Smoothened in complex with cyclopamine -

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Basic information

Entry
Database: PDB / ID: 6d32
TitleCrystal structure of Xenopus Smoothened in complex with cyclopamine
ComponentsSmoothened,Soluble cytochrome b562,Smoothened
KeywordsMEMBRANE PROTEIN / GPCR / Hedgehog signaling / Class Frizzled / Sterol
Function / homology
Function and homology information


tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / membrane => GO:0016020 / central nervous system development / electron transport chain / G protein-coupled receptor activity / cilium ...tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / membrane => GO:0016020 / central nervous system development / electron transport chain / G protein-coupled receptor activity / cilium / Wnt signaling pathway / electron transfer activity / periplasmic space / iron ion binding / dendrite / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Smoothened / Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled ...Smoothened / Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclopamine / Uncharacterized protein / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.751 Å
AuthorsHuang, P. / Zheng, S. / Kim, Y. / Kruse, A.C. / Salic, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM110041 United States
CitationJournal: Cell / Year: 2018
Title: Structural Basis of Smoothened Activation in Hedgehog Signaling.
Authors: Huang, P. / Zheng, S. / Wierbowski, B.M. / Kim, Y. / Nedelcu, D. / Aravena, L. / Liu, J. / Kruse, A.C. / Salic, A.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 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,Soluble cytochrome b562,Smoothened
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8083
Polymers68,9841
Non-polymers8232
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29580 Å2
Unit cell
Length a, b, c (Å)145.778, 79.232, 104.076
Angle α, β, γ (deg.)90.000, 108.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 68984.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog), (gene. exp.) Escherichia coli (E. coli)
Gene: smo, Smo, cybC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q98SW5, UniProt: P0ABE7, UniProt: A0A1L8GTP2*PLUS
#2: Chemical ChemComp-CY8 / Cyclopamine / (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol


Mass: 411.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H41NO2 / Comment: alkaloid*YM
Has protein modificationY

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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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 35-45% PEG 300, 300-500 mM LiSO4, 0.1 M MES pH 6-6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.74→49.63 Å / Num. obs: 11676 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.992 / Net I/σ(I): 6.1
Reflection shellResolution: 3.74→3.81 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 504 / CC1/2: 0.617 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L7D, 5KZY and 4O9R

5l7d

5kzy

4o9r


Resolution: 3.751→41.054 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.26 587 5.12 %
Rwork0.227 --
obs0.2287 11455 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.84 Å2 / Biso mean: 90.0449 Å2 / Biso min: 40.22 Å2
Refinement stepCycle: final / Resolution: 3.751→41.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 60 0 4596
Biso mean--124.48 --
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034726
X-RAY DIFFRACTIONf_angle_d0.846418
X-RAY DIFFRACTIONf_chiral_restr0.028721
X-RAY DIFFRACTIONf_plane_restr0.003800
X-RAY DIFFRACTIONf_dihedral_angle_d14.3481715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7506-4.12780.33921400.27522624276496
4.1278-4.72430.25271570.21582691284898
4.7243-5.94920.24311410.23472746288799
5.9492-41.05690.24371490.20922807295699

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