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- PDB-6t4y: ROR(gamma)t ligand binding domain in complex with 25-hydroxychole... -

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Basic information

Entry
Database: PDB / ID: 6t4y
TitleROR(gamma)t ligand binding domain in complex with 25-hydroxycholesterol and allosteric ligand MRL871
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 / 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-4F1 / 25-HYDROXYCHOLESTEROL / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)31,4544
Polymers30,5141
Non-polymers9403
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint0 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.509, 108.509, 105.040
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-4F1 / 4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-1H-indazol-3-yl}benzoic acid


Mass: 444.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H12ClF3N2O3 / 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.: 47 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.6M AmSO4 + 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: 1.95→105.04 Å / Num. obs: 50467 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.012 / Rrim(I) all: 0.073 / Net I/σ(I): 28.5
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.95-218900.6971
8.94-105.0436111

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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: 1.95→93.972 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2151 2562 5.08 %
Rwork0.1857 --
obs0.1872 50467 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.06 Å2 / Biso mean: 61.0044 Å2 / Biso min: 36.05 Å2
Refinement stepCycle: final / Resolution: 1.95→93.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 66 47 2093
Biso mean--50.67 57.05 -
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
1.95-1.98760.33771160.35422726
1.9876-2.02810.3361380.30812642
2.0281-2.07220.31171950.27962618
2.0722-2.12040.29211210.25292663
2.1204-2.17350.25771280.22692676
2.1735-2.23220.2781390.22372663
2.2322-2.29790.24231270.2132671
2.2979-2.37210.26641550.22650
2.3721-2.45690.21471290.1852659
2.4569-2.55530.21761420.1992653
2.5553-2.67160.22591360.20122671
2.6716-2.81240.2791810.212630
2.8124-2.98870.24951590.20162648
2.9887-3.21940.20941430.20122664
3.2194-3.54340.23241330.1922665
3.5434-4.05620.18121610.16782641
4.0562-5.11030.18931190.15012686
5.1103-93.9720.17751400.16972679
Refinement TLS params.Method: refined / Origin x: 5.6762 Å / Origin y: -39.8368 Å / Origin z: -4.6117 Å
111213212223313233
T0.3333 Å2-0.0648 Å2-0.0528 Å2-0.4179 Å20.0682 Å2--0.4082 Å2
L4.4309 °2-1.7977 °22.4316 °2-2.185 °2-1.7981 °2--2.861 °2
S0.2021 Å °0.3529 Å °-0.159 Å °0.042 Å °-0.1132 Å °0.1842 Å °0.043 Å °0.1368 Å °-0.0042 Å °
Refinement TLS groupSelection details: (chain A and resseq 267:507)

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