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- PDB-6t50: ROR(gamma)t ligand binding domain in complex with 25-hydroxychole... -

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Basic information

Entry
Database: PDB / ID: 6t50
TitleROR(gamma)t ligand binding domain in complex with 25-hydroxycholesterol and allosteric ligand Glenmark
ComponentsNuclear receptor ROR-gamma
KeywordsGENE REGULATION / Nuclear Receptor / Allosteric / Inverse Agonist / Inhibitor
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / 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 / 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 / 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 ...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 / 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
Similarity search - Domain/homology
25-HYDROXYCHOLESTEROL / Chem-MJE / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
Authorsde Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research024.001.035 Netherlands
Netherlands Organisation for Scientific Research016.150.366 Netherlands
European Union705188
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Cooperativity between the orthosteric and allosteric ligand binding sites of ROR gamma t.
Authors: de Vries, R.M.J.M. / Meijer, F.A. / Doveston, R.G. / Leijten-van de Gevel, I.A. / Brunsveld, L.
History
DepositionOct 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4404
Polymers30,5141
Non-polymers9263
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint2 kcal/mol
Surface area11830 Å2
Unit cell
Length a, b, c (Å)108.325, 108.325, 108.509
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: 30514.166 Da / Num. of mol.: 1
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-HC3 / 25-HYDROXYCHOLESTEROL / (3BETA)-CHOLEST-5-ENE-3,25-DIOL


Mass: 402.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MJE / 4-[1-[2,6-bis(chloranyl)phenyl]carbonyl-5-methyl-thieno[3,2-c]pyrazol-3-yl]benzoic acid


Mass: 431.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2 + 6% PEG6K + 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.87→108.51 Å / Num. obs: 58851 / % possible obs: 100 % / Redundancy: 39 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.009 / Rrim(I) all: 0.056 / Net I/σ(I): 35.8
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.87-1.9119690.7611
8.97-108.5136111

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMAC5refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SAL

6sal


Resolution: 1.87→93.812 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.73
RfactorNum. reflection% reflection
Rfree0.21 2950 5.01 %
Rwork0.1856 --
obs0.1867 58851 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.59 Å2 / Biso mean: 54.8692 Å2 / Biso min: 30.8 Å2
Refinement stepCycle: final / Resolution: 1.87→93.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 63 92 2135
Biso mean--42.73 53.76 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.90070.39441540.38332631
1.9007-1.93350.41271330.34982671
1.9335-1.96860.37921700.32092632
1.9686-2.00650.28671800.28442634
2.0065-2.04750.28761350.2522657
2.0475-2.0920.25661490.2462649
2.092-2.14070.25751210.21432668
2.1407-2.19420.28381520.20992644
2.1942-2.25350.23121290.2122694
2.2535-2.31980.21711310.20532672
2.3198-2.39470.2231380.20072665
2.3947-2.48030.18841140.18532668
2.4803-2.57960.20631210.19732716
2.5796-2.6970.23891380.19032639
2.697-2.83920.19131430.20272685
2.8392-3.01710.22061330.19122652
3.0171-3.25010.23621620.19672628
3.2501-3.57720.20431440.18432668
3.5772-4.09480.21491410.16482676
4.0948-5.1590.14521510.14792662
5.159-93.8120.21671110.17422690
Refinement TLS params.Method: refined / Origin x: 5.1765 Å / Origin y: -39.883 Å / Origin z: -5.2231 Å
111213212223313233
T0.3178 Å2-0.0549 Å2-0.0645 Å2-0.3944 Å20.0537 Å2--0.386 Å2
L4.3198 °2-1.6362 °22.3099 °2-1.7497 °2-1.8013 °2--2.666 °2
S0.2204 Å °0.4167 Å °-0.1892 Å °-0.0252 Å °-0.1148 Å °0.0768 Å °0.0777 Å °0.1676 Å °-0.0002 Å °
Refinement TLS groupSelection details: (chain A and resseq 267:507)

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