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- PDB-5v57: 3.0A SYN structure of the multi-domain human smoothened receptor ... -

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Basic information

Entry
Database: PDB / ID: 5v57
Title3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114
ComponentsSmoothened homolog,Flavodoxin,Smoothened homolog
KeywordsMEMBRANE PROTEIN / human smoothened receptor complex / GPCR Hedgehog signaling / GPCR / Class F / 7TM domain / hinge domain / extracellular cystein-rich domain / Flavodoxin / LCP / synchrotron radiation / TC114
Function / homology
Function and homology information


ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / response to inositol / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / response to inositol / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling / myoblast migration / atrial septum morphogenesis / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / left/right axis specification / Activation of SMO / ciliary tip / patched binding / forebrain morphogenesis / type B pancreatic cell development / somite development / positive regulation of organ growth / dorsal/ventral neural tube patterning / BBSome-mediated cargo-targeting to cilium / smooth muscle tissue development / cerebellar cortex morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / cellular response to cholesterol / pattern specification process / mammary gland epithelial cell differentiation / dentate gyrus development / commissural neuron axon guidance / thalamus development / dopaminergic neuron differentiation / central nervous system neuron differentiation / oxysterol binding / positive regulation of multicellular organism growth / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / cell fate specification / cAMP-dependent protein kinase inhibitor activity / neural crest cell migration / negative regulation of DNA binding / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / ciliary membrane / hair follicle morphogenesis / midgut development / smoothened signaling pathway / negative regulation of epithelial cell differentiation / positive regulation of neuroblast proliferation / heart looping / protein kinase A catalytic subunit binding / endoplasmic reticulum-Golgi intermediate compartment / odontogenesis of dentin-containing tooth / negative regulation of protein phosphorylation / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / centriole / homeostasis of number of cells within a tissue / protein sequestering activity / positive regulation of epithelial cell proliferation / central nervous system development / epithelial cell proliferation / astrocyte activation / G protein-coupled receptor activity / Hedgehog 'on' state / cerebral cortex development / positive regulation of protein import into nucleus / multicellular organism growth / protein import into nucleus / osteoblast differentiation / endocytic vesicle membrane / late endosome / FMN binding / in utero embryonic development / gene expression / electron transfer activity / protein stabilization / cilium / positive regulation of cell migration / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Flavodoxin, short chain / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein ...Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Flavodoxin, short chain / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Flavodoxin, conserved site / Flavodoxin signature. / 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. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-836 / FLAVIN MONONUCLEOTIDE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Flavodoxin / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. ...Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F.
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand.
Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / ...Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 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 1.3Nov 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 homolog,Flavodoxin,Smoothened homolog
B: Smoothened homolog,Flavodoxin,Smoothened homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6467
Polymers144,2982
Non-polymers2,3485
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-12 kcal/mol
Surface area60320 Å2
Unit cell
Length a, b, c (Å)40.080, 356.360, 59.090
Angle α, β, γ (deg.)90.00, 102.79, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Smoothened homolog,Flavodoxin,Smoothened homolog / SMO / Protein Gx


Mass: 72149.023 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 58-433,444-558 / Mutation: P2A, Y98W
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Smoothened homolog (RESIDUES 58-433), Flavodoxin (RESIDUES 1002-1148), Smoothened homolog (RESIDUES 444-558) and 10 HIS tags
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris (bacteria)
Gene: SMO, SMOH, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Production host: Homo sapiens (human) / References: UniProt: Q99835, UniProt: P00323
#2: Chemical ChemComp-836 / N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide


Mass: 539.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24F3N7O3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG 400, 50-200 mM Ammonium nitrate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.38 Å / Num. obs: 29571 / % possible obs: 91.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 72.64 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.9 / % possible all: 81.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V56

5v56


Resolution: 3→48.38 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1502 5.08 %RANDOM
Rwork0.203 ---
obs0.205 29552 91.9 %-
Displacement parametersBiso mean: 82.72 Å2
Baniso -1Baniso -2Baniso -3
1-4.083 Å20 Å2-0.1952 Å2
2--4.3715 Å20 Å2
3----8.4546 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: 1 / Resolution: 3→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9949 0 152 0 10101
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910394HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9314193HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d4568SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes210HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1591HARMONIC5
X-RAY DIFFRACTIONt_it10394HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion1.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1327SEMIHARMONIC5
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_contact12250SEMIHARMONIC4
LS refinement shellResolution: 3→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.23 113 4.41 %
Rwork0.216 2448 -
all0.216 2561 -
obs--79.47 %
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)
10.54721.08640.14511.92010.36920.20660.05050.02950.14550.0774-0.0570.0341-0.146-0.04050.0065-0.1396-0.0096-0.0389-0.10850.00640.1022-43.19-8.30227.355
20.78231.117-0.03831.8027-0.08430.07160.11620.0062-0.20040.2224-0.1224-0.10060.14870.01440.0062-0.0511-0.0385-0.0199-0.1262-0.03070.0072-96.753-100.41150.894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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