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- PDB-5ixk: RORgamma in complex with inverse agonist BIO399. -

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Basic information

Entry
Database: PDB / ID: 5ixk
TitleRORgamma in complex with inverse agonist BIO399.
ComponentsNuclear receptor ROR-gamma
KeywordsIMMUNE SYSTEM / RORgamma / Nuclear hormone receptor / Inverse agonist / AF2 helix
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6EW / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMarcotte, D.J.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.
Authors: Marcotte, D.J. / Liu, Y. / Little, K. / Jones, J.H. / Powell, N.A. / Wildes, C.P. / Silvian, L.F. / Chodaparambil, J.V.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0844
Polymers53,1152
Non-polymers9692
Water70339
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A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0422
Polymers26,5581
Non-polymers4851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0422
Polymers26,5581
Non-polymers4851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.939, 56.167, 78.752
Angle α, β, γ (deg.)90.000, 124.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

DetailsMonomer confirmed by SEC

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 26557.652 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain UNP Residue 268-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51449
#2: Chemical ChemComp-6EW / N-(5-ethyl-3,3-dimethyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-8-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide


Mass: 484.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27F3N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M BisTRIS pH 5.5 0.2M NH3 Acetate 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→64.69 Å / Num. obs: 18850 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Net I/av σ(I): 16.698 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.35-2.393.30.437199.9
2.39-2.433.30.4131100
2.43-2.483.30.4151100
2.48-2.533.30.373199.8
2.53-2.593.30.3171100
2.59-2.653.30.2961100
2.65-2.713.30.274199.9
2.71-2.793.40.2261100
2.79-2.873.40.21100
2.87-2.963.40.19199.9
2.96-3.073.30.181100
3.07-3.193.30.1441100
3.19-3.333.30.126199.9
3.33-3.513.30.118199.7
3.51-3.733.20.105199.9
3.73-4.023.20.084199.4
4.02-4.423.20.069199.6
4.42-5.063.30.057199.6
5.06-6.373.30.05199.9
6.37-103.10.04192.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LOL

3lol
PDB Unreleased entry


Resolution: 2.35→64.69 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 21.843 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.284
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 970 5.2 %RANDOM
Rwork0.211 ---
obs0.2137 17766 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.17 Å2 / Biso mean: 50.457 Å2 / Biso min: 29.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å2-0 Å21.04 Å2
2---5.25 Å2-0 Å2
3---3.73 Å2
Refinement stepCycle: final / Resolution: 2.35→64.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 66 39 3562
Biso mean--63.41 52.15 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193616
X-RAY DIFFRACTIONr_bond_other_d0.0030.023393
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9684904
X-RAY DIFFRACTIONr_angle_other_deg1.46837743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89923.69168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97915613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.341522
X-RAY DIFFRACTIONr_chiral_restr0.1240.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024106
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02888
X-RAY DIFFRACTIONr_mcbond_it2.5121.8991761
X-RAY DIFFRACTIONr_mcbond_other2.5121.8981760
X-RAY DIFFRACTIONr_mcangle_it3.8762.8362200
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 59 -
Rwork0.214 1316 -
all-1375 -
obs--98.43 %
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)
11.3554-0.08190.47930.2211-0.12940.21870.039-0.0581-0.0888-0.0105-0.00050.0072-0.0179-0.0137-0.03850.5167-0.00160.08250.53770.01560.0202-16.5095-0.1951-15.8545
21.03490.4413-0.18560.7862-0.24070.07980.0313-0.0413-0.098-0.0127-0.0449-0.0499-0.03450.0020.01360.509-0.0080.07460.50970.00260.021214.342817.0847-16.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A269 - 487
2X-RAY DIFFRACTION2B268 - 487

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