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- PDB-7np5: ROR(gamma)t ligand binding domain in complex with allosteric liga... -

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Basic information

Entry
Database: PDB / ID: 7np5
TitleROR(gamma)t ligand binding domain in complex with allosteric ligand FM216
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Nuclear receptor / Retinoic acid receptor-related orphan receptor gamma t / inverse agonist
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / adipose tissue development / lymph node development / xenobiotic metabolic process / circadian regulation of gene expression / Nuclear Receptor transcription pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / 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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Domain/homology
Chem-UKB / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOerlemans, G.J.M. / Somsen, B.A. / de Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L.
Funding support Netherlands, 5items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
Netherlands Organisation for Scientific Research (NWO)016.150.366 Netherlands
Netherlands Organisation for Scientific Research (NWO)711.018.003 Netherlands
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
European Union (EU)705188 Netherlands
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Activity Relationship Studies of Trisubstituted Isoxazoles as Selective Allosteric Ligands for the Retinoic-Acid-Receptor-Related Orphan Receptor gamma t.
Authors: Meijer, F.A. / Saris, A.O.W.M. / Doveston, R.G. / Oerlemans, G.J.M. / de Vries, R.M.J.M. / Somsen, B.A. / Unger, A. / Klebl, B. / Ottmann, C. / Cossar, P.J. / Brunsveld, L.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2372
Polymers28,7561
Non-polymers4811
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.223, 108.223, 98.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 28756.293 Da / Num. of mol.: 1 / Mutation: C455H
Source method: isolated from a genetically manipulated source
Details: First four residues (GSHM) are from expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P51449
#2: Chemical ChemComp-UKB / 4-[[3-[2-chloranyl-6-(trifluoromethyl)phenyl]-5-(1~{H}-pyrrol-3-yl)-1,2-oxazol-4-yl]methoxy]-2-fluoranyl-benzoic acid


Mass: 480.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H13ClF4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.6M AmSO4 + 0.1M Tris (pH8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968626 Å / Relative weight: 1
ReflectionResolution: 1.55→68 Å / Num. obs: 49800 / % possible obs: 99.9 % / Redundancy: 37.3 % / CC1/2: 1 / Net I/σ(I): 18.3
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 2412 / CC1/2: 0.386

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
Aimless7.1.010data reduction
DIALS7.1.010data scaling
MOLREPphasing
Coot0.8.9.2model building
REFMAC7.1.010refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SAL

6sal


Resolution: 1.55→43.7 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 4759 5.11 %
Rwork0.234 88351 -
obs0.2358 49800 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.26 Å2 / Biso mean: 40.0738 Å2 / Biso min: 24.1 Å2
Refinement stepCycle: final / Resolution: 1.55→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 33 123 2115
Biso mean--30.47 47.2 -
Num. residues----242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.4541680.4362717288591
1.57-1.590.41041700.42062881305198
1.59-1.610.43831490.40272893304299
1.61-1.630.38231570.40182960311799
1.63-1.650.38561490.4022968311799
1.65-1.670.38421630.36732930309399
1.67-1.690.39911370.37442978311599
1.69-1.720.38421880.34992952314099
1.72-1.750.41081690.39052905307499
1.75-1.770.4211620.389229433105100
1.77-1.810.38551530.370629823135100
1.81-1.840.35871650.360829393104100
1.84-1.870.4041820.31929283110100
1.87-1.910.31032060.317328963102100
1.91-1.950.36631540.298629873141100
1.95-20.34581560.277829953151100
2-2.050.31571490.273529403089100
2.05-2.10.33641520.270529763128100
2.1-2.170.32261520.252629813133100
2.17-2.240.31041570.235729483105100
2.24-2.320.31921740.2429523126100
2.32-2.410.28711730.233230013174100
2.41-2.520.27931240.219329913115100
2.52-2.650.26221280.217830033131100
2.65-2.820.26181600.222429733133100
2.82-3.030.23491590.211929483107100
3.04-3.340.23091580.212629883146100
3.34-3.820.20371600.203129603120100
3.82-4.810.18571350.18529813116100
4.82-43.70.30741500.23222855300596

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