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- PDB-6q2w: Crystal structure of human ROR gamma LBD in complex with a quinol... -

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Basic information

Entry
Database: PDB / ID: 6q2w
TitleCrystal structure of human ROR gamma LBD in complex with a quinoline sulfonamide inverse agonist
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / ROR gamma / inverse agonist / nuclear hormone receptor
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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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-HBW / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsCiesielski, F. / Amaudrut, J. / Argiriadi, M.A. / Barth, M. / Breinlinger, E.C. / Calderwood, D.J. / Cusack, K.P. / Kort, M.E. / Montalbetti, C. / Potin, D. ...Ciesielski, F. / Amaudrut, J. / Argiriadi, M.A. / Barth, M. / Breinlinger, E.C. / Calderwood, D.J. / Cusack, K.P. / Kort, M.E. / Montalbetti, C. / Potin, D. / Poupardin, O. / Spitzer, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Discovery of novel quinoline sulphonamide derivatives as potent, selective and orally active ROR gamma inverse agonists.
Authors: Amaudrut, J. / Argiriadi, M.A. / Barth, M. / Breinlinger, E.C. / Bressac, D. / Broqua, P. / Calderwood, D.J. / Chatar, M. / Cusack, K.P. / Gauld, S.B. / Jacquet, S. / Kamath, R.V. / Kort, M. ...Authors: Amaudrut, J. / Argiriadi, M.A. / Barth, M. / Breinlinger, E.C. / Bressac, D. / Broqua, P. / Calderwood, D.J. / Chatar, M. / Cusack, K.P. / Gauld, S.B. / Jacquet, S. / Kamath, R.V. / Kort, M.E. / Lepais, V. / Luccarini, J.M. / Masson, P. / Montalbetti, C. / Mounier, L. / Potin, D. / Poupardin, O. / Rouaud, S. / Spitzer, L. / Wallace, C.D.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / pdbx_database_proc
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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)52,9734
Polymers51,7162
Non-polymers1,2572
Water3,117173
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4862
Polymers25,8581
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4862
Polymers25,8581
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.120, 56.200, 81.400
Angle α, β, γ (deg.)90.000, 125.060, 90.000
Int Tables number5
Space group name H-MC121

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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: 25857.949 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-HBW / (2~{S})-1-[2,4-bis(chloranyl)-3-[[4-imidazol-1-yl-2-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]sulfonyl-~{N}-methyl-pyrrolidine-2-carboxamide


Mass: 628.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22Cl2F3N5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M MgCl2, 0.1M Mes pH 6, 8% w/v PEG 6000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.99→46.2 Å / Num. obs: 32496 / % possible obs: 99.1 % / Redundancy: 3.678 % / Biso Wilson estimate: 36.172 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.09 / Χ2: 1.063 / Net I/σ(I): 10.1 / Num. measured all: 119530
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.113.4520.3262.6351060.9610.38397.4
2.11-2.253.7620.2634.0549320.9710.30699.6
2.25-2.433.7740.1895.9845580.9780.2299.7
2.43-2.663.8040.1298.4742500.9870.1599.5
2.66-2.983.7450.09311.6638400.9910.10899.7
2.98-3.433.6640.07315.6733850.9920.08599.3
3.43-4.23.6620.05819.7828720.9930.06899.4
4.2-5.913.6190.05421.622580.9940.06398.9
5.91-46.23.4830.04821.8712950.9960.05798

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.78 Å46.2 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0W

3b0w


Resolution: 1.99→46.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.533 / SU ML: 0.145 / SU R Cruickshank DPI: 0.1891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1625 5 %RANDOM
Rwork0.1873 ---
obs0.1896 30868 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.25 Å2 / Biso mean: 39.927 Å2 / Biso min: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å20.1 Å2
2---1.81 Å20 Å2
3---2.83 Å2
Refinement stepCycle: final / Resolution: 1.99→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 82 173 3824
Biso mean--52.22 46.55 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173465
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6685078
X-RAY DIFFRACTIONr_angle_other_deg1.381.5877999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6825449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18420.791215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5331534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
LS refinement shellResolution: 1.986→2.037 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 113 -
Rwork0.35 2143 -
all-2256 -
obs--95.23 %

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