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- PDB-6d35: Crystal structure of Xenopus Smoothened in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 6d35
TitleCrystal structure of Xenopus Smoothened in complex with cholesterol
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 / Wnt signaling pathway ...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 / Wnt signaling pathway / periplasmic space / electron transfer activity / cilium / iron ion binding / heme binding / dendrite / 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
CHOLESTEROL / 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: 3.9 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 20, 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)67,9552
Polymers67,5691
Non-polymers3871
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint1 kcal/mol
Surface area30100 Å2
Unit cell
Length a, b, c (Å)147.551, 77.262, 103.343
Angle α, β, γ (deg.)90.000, 108.310, 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: 67568.766 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-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
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: 4.14 Å3/Da / Density % sol: 70.28 %
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: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 8172 / % possible obs: 79.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 81.04 Å2 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.139 / Rrim(I) all: 0.239 / Χ2: 1.495 / Net I/σ(I): 5 / Num. measured all: 18197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.9-3.971.50.5263080.4740.4660.7060.58660.2
3.97-4.041.50.653070.4120.5710.8680.65561
4.04-4.121.60.7053240.3530.640.9550.78764.2
4.12-4.21.60.4543580.6030.3820.5960.91269
4.2-4.291.80.4133260.6740.3340.5330.70264.7
4.29-4.391.70.4583470.5780.3830.6011.05467.4
4.39-4.51.70.3523560.7380.2860.4561.26571.3
4.5-4.621.90.3323840.7760.2650.4271.53472
4.62-4.7620.2933550.8180.2220.3691.41672.6
4.76-4.9120.2674100.8590.2060.3391.47977.2
4.91-5.0920.2393920.9050.1820.3021.3178.7
5.09-5.2920.2754220.8480.2010.3431.35882.4
5.29-5.532.10.3264590.8580.2350.4041.10988.6
5.53-5.822.20.3394640.7880.2490.4240.69591
5.82-6.192.40.3584740.8080.2470.4380.79391.5
6.19-6.662.60.2874900.8830.1980.3511.07195.1
6.66-7.333.10.2045050.9550.1260.2411.22897.3
7.33-8.393.30.1485170.9720.0890.1741.87397.5
8.39-10.553.10.14900.9880.0650.122.3492.8
10.55-502.90.0684840.9920.0470.0843.10489.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D32

6d32


Resolution: 3.9→36.098 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3045 810 10.02 %
Rwork0.2525 7277 -
obs0.2577 8087 79.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.78 Å2 / Biso mean: 82.509 Å2 / Biso min: 25.73 Å2
Refinement stepCycle: final / Resolution: 3.9→36.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 28 0 4616
Biso mean--104.15 --
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034741
X-RAY DIFFRACTIONf_angle_d0.6566428
X-RAY DIFFRACTIONf_chiral_restr0.025719
X-RAY DIFFRACTIONf_plane_restr0.003806
X-RAY DIFFRACTIONf_dihedral_angle_d13.1091700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9005-4.14450.34591020.2922910101260
4.1445-4.4640.34231140.27511025113968
4.464-4.91220.2781270.23491141126874
4.9122-5.62070.3371430.27251287143084
5.6207-7.07280.3281590.28311435159494
7.0728-36.09970.26631650.21851479164494

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