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- PDB-5kzv: Crystal structure of the xenopus Smoothened cysteine-rich domain ... -

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Basic information

Entry
Database: PDB / ID: 5kzv
TitleCrystal structure of the xenopus Smoothened cysteine-rich domain (CRD) in complex with 20(S)-hydroxycholesterol
ComponentsSmoothened
KeywordsSIGNALING PROTEIN / Hedgehog signaling / GPCR / cysteine-rich domain / sterol
Function / homology
Function and homology information


tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / central nervous system development / G protein-coupled receptor activity / cilium / dendrite / metal ion 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
(3alpha,8alpha)-cholest-5-ene-3,20-diol / Protein smoothened
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.616 Å
AuthorsHuang, P. / Kim, Y. / Salic, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM092924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM110041 United States
CitationJournal: Cell / Year: 2016
Title: Cellular Cholesterol Directly Activates Smoothened in Hedgehog Signaling.
Authors: Huang, P. / Nedelcu, D. / Watanabe, M. / Jao, C. / Kim, Y. / Liu, J. / Salic, A.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Smoothened
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3942
Polymers13,9911
Non-polymers4031
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.248, 28.349, 61.929
Angle α, β, γ (deg.)90.000, 104.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

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Components

#1: Protein Smoothened


Mass: 13991.058 Da / Num. of mol.: 1 / Fragment: UNP Residues 35-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Smo / Production host: Escherichia coli (E. coli) / References: UniProt: Q98SW5
#2: Chemical ChemComp-HCD / (3alpha,8alpha)-cholest-5-ene-3,20-diol / 20S-hydroxycholesterol


Mass: 402.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.15M potassium bromide and 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 14974 / % possible obs: 93 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.069 / Rrim(I) all: 0.143 / Χ2: 0.862 / Net I/av σ(I): 10.071 / Net I/σ(I): 9.2 / Num. measured all: 53587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.631.60.5994660.4930.5050.7870.92357.2
1.63-1.661.70.4945200.6930.4040.6410.75765.5
1.66-1.691.90.4456240.6540.3620.5770.8677.9
1.69-1.722.30.546550.7990.3970.6740.97483.4
1.72-1.762.80.4367130.8460.280.5210.92888.1
1.76-1.83.10.4577360.8520.2760.5370.95494.1
1.8-1.853.40.3748120.8760.2180.4361.04599.6
1.85-1.93.60.347670.9080.1990.3960.96599.7
1.9-1.953.80.2758000.9510.1550.3170.94499.9
1.95-2.023.90.2317990.960.1290.2660.89799.9
2.02-2.0940.2197940.960.1210.2510.89699.7
2.09-2.174.10.1838170.9680.10.210.92399.6
2.17-2.274.10.1597860.9760.0860.1820.95599.9
2.27-2.394.20.1398040.9730.0750.1580.83199.9
2.39-2.544.20.1158150.9790.0620.1310.71999.9
2.54-2.744.10.1067990.9840.0560.120.712100
2.74-3.014.10.0928090.9860.0490.1050.652100
3.01-3.454.20.098170.9830.0470.1020.62599.2
3.45-4.344.10.0918120.9780.0490.1030.6999
4.34-5040.1158290.9620.0650.1331.17996.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C79

4c79


Resolution: 1.616→34.503 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 679 4.96 %
Rwork0.1741 13009 -
obs0.1757 13688 84.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.49 Å2 / Biso mean: 21.2164 Å2 / Biso min: 3.73 Å2
Refinement stepCycle: final / Resolution: 1.616→34.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 29 235 1167
Biso mean--13.65 34.83 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007962
X-RAY DIFFRACTIONf_angle_d1.3071310
X-RAY DIFFRACTIONf_chiral_restr0.053151
X-RAY DIFFRACTIONf_plane_restr0.006161
X-RAY DIFFRACTIONf_dihedral_angle_d13.577372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6161-1.74090.226790.20261470154948
1.7409-1.91610.22921330.18452399253280
1.9161-2.19330.21751640.16972982314698
2.1933-2.76310.21871560.17830523208100
2.7631-34.51130.1881470.16883106325398
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)
10.55140.45230.64271.34520.62830.7606-0.2018-0.49930.07380.0492-0.06470.1121-0.0491-0.0649-0.05430.14290.0278-0.00190.2874-0.0660.14682.773.188750.836
20.26970.08870.0630.6017-0.00760.5187-0.01410.0321-0.014-0.0241-0.00550.17520.0068-0.0803-0.01350.0671-0.00280.00550.0652-0.00740.04528.72610.15236.7052
30.92810.1657-0.83860.4136-0.20210.7679-0.1491-0.0267-0.03530.10810.012-0.12480.16150.1043-0.26750.0509-0.001-0.01140.0815-0.01590.050819.8825-1.182338.9392
41.421-0.3884-1.46140.5670.63522.0175-0.1595-0.0617-0.1343-0.0035-0.03570.08730.1551-0.3763-0.69450.08970.02620.01310.15820.01260.05466.449-0.551950.0898
50.0607-0.0097-0.10080.2197-0.00460.1693-0.0854-0.03530.05810.0009-0.0478-0.18780.0249-0.0336-0.01420.09360.0045-0.02750.11670.01580.117525.65556.084241.859
60.1428-0.00760.08340.0793-0.03010.06430.06670.07140.1549-0.0705-0.10690.0840.0203-0.0603-0.0140.11660.0154-0.02820.0978-0.02330.126118.255611.847940.0653
70.88880.4733-0.18080.7764-0.10690.08650.1274-0.3023-0.06580.1868-0.0856-0.0636-0.00950.1120.22480.24430.0553-0.06270.2339-0.03680.019716.95757.551952.9425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 45 )A36 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 87 )A46 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 103 )A88 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 116 )A104 - 116
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 133 )A117 - 133
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 140 )A134 - 140
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 152 )A141 - 152

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