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- PDB-6fgq: Ligand complex of RORg LBD -

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Basic information

Entry
Database: PDB / ID: 6fgq
TitleLigand complex of RORg LBD
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / RAR-related Orphan Receptor-g (RORg) / RORG LIGAND / STRUCTURE-BASED DESIGN
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-D9N / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
AuthorsXue, Y. / Aagaard, A. / Narjes, F.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Potent and Orally Bioavailable Inverse Agonists of ROR gamma t Resulting from Structure-Based Design.
Authors: Narjes, F. / Xue, Y. / von Berg, S. / Malmberg, J. / Llinas, A. / Olsson, R.I. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Hossain, N. / Lepisto, M. / Thunberg, L. / Leek, H. / Aagaard, ...Authors: Narjes, F. / Xue, Y. / von Berg, S. / Malmberg, J. / Llinas, A. / Olsson, R.I. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Hossain, N. / Lepisto, M. / Thunberg, L. / Leek, H. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Back, E. / Tangefjord, S. / Chen, R. / Xiong, Y. / Hongbin, G. / Hansson, T.G.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)62,9384
Polymers61,8372
Non-polymers1,1012
Water2,540141
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4692
Polymers30,9181
Non-polymers5511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4692
Polymers30,9181
Non-polymers5511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.550, 99.550, 129.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: 30918.490 Da / Num. of mol.: 2
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) / References: UniProt: P51449
#2: Chemical ChemComp-D9N / methyl 4-[[3-[5-[2-(4-ethylsulfonylphenyl)ethanoylamino]thiophen-3-yl]pyridin-2-yl]oxymethyl]benzoate


Mass: 550.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N2O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.3M LiSO4 0.1M MgCl2 0.1M Hepes pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.37→49.77 Å / Num. obs: 29472 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 70.61 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14
Reflection shellResolution: 2.37→2.45 Å

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Processing

SoftwareName: BUSTER / Version: 2.11.7 PACIOREK / Classification: refinement
RefinementResolution: 2.37→40.64 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1492 5.07 %RANDOM
Rwork0.212 ---
obs0.214 29420 99.7 %-
Displacement parametersBiso mean: 65.16 Å2
Baniso -1Baniso -2Baniso -3
1--3.2566 Å20 Å20 Å2
2---3.2566 Å20 Å2
3---6.5132 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.37→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 76 141 3827
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013764HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145064HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1372SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes569HARMONIC5
X-RAY DIFFRACTIONt_it3764HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion20.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion457SEMIHARMONIC5
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_contact4204SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.45 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2556 128 4.63 %
Rwork0.2469 2636 -
all0.2473 2764 -
obs--97.29 %
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)
10.9039-0.60840.25242.7082-1.62371.6422-0.0630.0530.0302-0.01030.0148-0.06270.05560.01640.0483-0.1403-0.0128-0.0394-0.06170.0554-0.0657-22.5428-30.53571.3164
22.60320.29951.55850.98780.72431.92760.0352-0.0016-0.0175-0.0547-0.14210.0220.0123-0.06120.1069-0.06650.0141-0.0145-0.1169-0.0316-0.0921-18.7586-31.8006-34.1683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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