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- PDB-5l7d: Structure of human Smoothened in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 5l7d
TitleStructure of human Smoothened in complex with cholesterol
ComponentsSmoothened homolog,Soluble cytochrome b562,Smoothened homolog
KeywordsMEMBRANE PROTEIN / G protein coupled receptor / morphogen signaling / Hedgehog signaling / cholesterol / signaling protein
Function / homology
Function and homology information


ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / 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 ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / 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 / contact inhibition / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / left/right axis specification / ciliary tip / Activation of SMO / patched binding / thalamus development / somite development / type B pancreatic cell development / forebrain morphogenesis / cellular response to cholesterol / dorsal/ventral neural tube patterning / BBSome-mediated cargo-targeting to cilium / positive regulation of organ growth / positive regulation of branching involved in ureteric bud morphogenesis / smooth muscle tissue development / pattern specification process / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / positive regulation of multicellular organism growth / dopaminergic neuron differentiation / commissural neuron axon guidance / oxysterol binding / 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 / ciliary membrane / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / negative regulation of epithelial cell differentiation / midgut development / smoothened signaling pathway / hair follicle morphogenesis / positive regulation of neuroblast proliferation / heart looping / negative regulation of DNA binding / odontogenesis of dentin-containing tooth / protein kinase A catalytic subunit binding / endoplasmic reticulum-Golgi intermediate compartment / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / homeostasis of number of cells within a tissue / centriole / protein sequestering activity / negative regulation of protein phosphorylation / epithelial cell proliferation / central nervous system development / electron transport chain / G protein-coupled receptor activity / positive regulation of epithelial cell proliferation / astrocyte activation / Hedgehog 'on' state / multicellular organism growth / cilium / cerebral cortex development / positive regulation of protein import into nucleus / osteoblast differentiation / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / in utero embryonic development / periplasmic space / electron transfer activity / protein stabilization / positive regulation of cell migration / iron ion binding / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / dendrite / heme binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular exosome / 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. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsByrne, E.F.X. / Sircar, R. / Miller, P.S. / Hedger, G. / Luchetti, G. / Nachtergaele, S. / Tully, M.D. / Mydock-McGrane, L. / Covey, D.F. / Rambo, R.P. ...Byrne, E.F.X. / Sircar, R. / Miller, P.S. / Hedger, G. / Luchetti, G. / Nachtergaele, S. / Tully, M.D. / Mydock-McGrane, L. / Covey, D.F. / Rambo, R.P. / Sansom, M.S.P. / Newstead, S. / Rohatgi, R. / Siebold, C.
CitationJournal: Nature / Year: 2016
Title: Structural basis of Smoothened regulation by its extracellular domains.
Authors: Byrne, E.F. / Sircar, R. / Miller, P.S. / Hedger, G. / Luchetti, G. / Nachtergaele, S. / Tully, M.D. / Mydock-McGrane, L. / Covey, D.F. / Rambo, R.P. / Sansom, M.S. / Newstead, S. / Rohatgi, R. / Siebold, C.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,4437
Polymers141,5682
Non-polymers8755
Water0
1
A: Smoothened homolog,Soluble cytochrome b562,Smoothened homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6596
Polymers70,7841
Non-polymers8755
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Smoothened homolog,Soluble cytochrome b562,Smoothened homolog


Theoretical massNumber of molelcules
Total (without water)70,7841
Polymers70,7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.900, 63.020, 208.590
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 70783.969 Da / Num. of mol.: 2
Fragment: UNP residues 32-428,UNP residues 23-127,UNP residues 443-555
Source method: isolated from a genetically manipulated source
Details: Human Smoothened with an soluble E. coli cytochrome b562 protein replacing Smoothened residues 429 to 445.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: SMO, SMOH, cybC / Plasmid: pHLsec / Cell line (production host): HEK-293S-GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q99835, UniProt: P0ABE7
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M MES pH 6, 30% (v/v) PEG500 DME, 0.1 M sodium acetate, 0.5 mM zinc chloride, 0.1 M ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→61 Å / Num. obs: 25214 / % possible obs: 93.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 76.23 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.305 / Net I/av σ(I): 4.3 / Net I/σ(I): 4.3
Reflection shellResolution: 3.2→3.41 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.6 / % possible all: 78.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qim

4qim


Resolution: 3.2→29.33 Å / Cor.coef. Fo:Fc: 0.8947 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.504
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1302 5.18 %RANDOM
Rwork0.23 ---
obs0.2318 25151 94.58 %-
Displacement parametersBiso mean: 137.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.6415 Å20 Å2-23.5459 Å2
2---25.0814 Å20 Å2
3---11.4399 Å2
Refine analyzeLuzzati coordinate error obs: 0.628 Å
Refinement stepCycle: 1 / Resolution: 3.2→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 58 0 9265
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089525HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.912971HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4307SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1390HARMONIC5
X-RAY DIFFRACTIONt_it9525HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion2.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1237SEMIHARMONIC5
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_contact10952SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.33 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2372 95 4.36 %
Rwork0.2584 2086 -
all0.2576 2181 -
obs--72.86 %
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)
17.719-0.0448-2.28335.2841-1.09177.8227-0.0331-0.2428-0.38010.0453-0.0301-0.2783-0.0232-0.14630.0632-0.03360.0945-0.0188-0.2889-0.02540.0931-46.0203-3.9808107.8299
20.16150.8072-0.47230.1016-0.42561.4860.01660.0175-0.0266-0.0139-0.01350.0930.1228-0.0195-0.0031-0.11040.06220.10180.13960.0258-0.0189-41.25947.33985.4941
31.6166-0.0818-0.44380.7908-0.70015.62720.04440.5113-0.07710.00410.10040.0301-0.0983-0.5741-0.1448-0.17520.03380.04210.32940.0893-0.2687-29.395110.66556.6725
42.4756-1.59470.51721.80241.4683.3058-0.0037-0.0127-0.0227-0.0643-0.02730.0463-0.0015-0.00680.031-0.06170.00170.22280.3339-0.0976-0.13091.1285-8.413113.1706
56.6941-1.0329-1.23330.0051-1.07914.9280.0492-0.011-0.1456-0.1723-0.0512-0.077-0.0317-0.02640.0019-0.0074-0.03810.18210.37340.0097-0.223522.830914.1804-5.2432
60.8473-0.5452-0.7060-0.6271.9485-0.00660.02630.0447-0.00320.006-0.04160.0044-0.00780.00060.028-0.05020.09750.26120.0682-0.170113.13823.896916.524
72.48080.2053-0.35190.7870.28823.07390.06120.4426-0.20680.02110.0342-0.1518-0.41390.1398-0.0955-0.2244-0.14490.08420.47530.1682-0.34721.443120.631847.9173
86.6163.4513-2.99374.0122-2.92513.62420.02410.2293-0.0770.0528-0.133-0.06590.08910.28910.10890.0909-0.1265-0.0443-0.1507-0.07480.019-13.5375-9.792290.562
90.6195-0.0072-0.28410-0.7273-0.07450.00170.0080.0154-0.0225-0.00050.0002-0.0096-0.0011-0.0013-0.0656-0.05370.01670.04560.07590.0437-34.4722-2.236598.9728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|58 - A|190 }
2X-RAY DIFFRACTION2{ A|191 - A|216 }
3X-RAY DIFFRACTION3{ A|217 - A|553 }
4X-RAY DIFFRACTION4{ A|1011 - A|1131 }
5X-RAY DIFFRACTION5{ B|58 - B|190 }
6X-RAY DIFFRACTION6{ B|191 - B|216 }
7X-RAY DIFFRACTION7{ B|217 - B|551 }
8X-RAY DIFFRACTION8{ B|1011 - B|1131 }
9X-RAY DIFFRACTION9{ D|1 }

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