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- PDB-6t4x: ROR(gamma)t ligand binding domain in complex with 25-hydroxychole... -

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Basic information

Entry
Database: PDB / ID: 6t4x
TitleROR(gamma)t ligand binding domain in complex with 25-hydroxycholesterol and allosteric ligand FM26
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
25-HYDROXYCHOLESTEROL / Chem-L3E / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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)31,4694
Polymers30,5141
Non-polymers9553
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint1 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.880, 108.880, 98.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

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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-L3E / 4-[(~{E})-[3-[2-chloranyl-6-(trifluoromethyl)phenyl]-5-(1~{H}-pyrrol-3-yl)-1,2-oxazol-4-yl]methylideneamino]benzoic acid


Mass: 459.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H13ClF3N3O3 / 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.: 255 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
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: 1.48→98.54 Å / Num. obs: 108984 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.018 / Rrim(I) all: 0.084 / Net I/σ(I): 25.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.48-1.5127970.7571
8.11-98.5444911

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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: 1.48→94.293 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.41
RfactorNum. reflection% reflection
Rfree0.1852 5383 4.94 %
Rwork0.1749 --
obs0.1754 108984 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.7 Å2 / Biso mean: 30.237 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 1.48→94.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 73 255 2304
Biso mean--23.08 42.38 -
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
1.48-1.49680.3211710.2953467
1.4968-1.51440.25931530.29063521
1.5144-1.53290.34941680.28583435
1.5329-1.55230.28721890.26213441
1.5523-1.57280.30811420.24673471
1.5728-1.59430.26981790.24723493
1.5943-1.61710.22361380.23433457
1.6171-1.64120.23041870.22793437
1.6412-1.66690.24991980.22033437
1.6669-1.69420.2442050.22413444
1.6942-1.72340.27121730.22333440
1.7234-1.75480.2191900.21793458
1.7548-1.78850.21791900.19833466
1.7885-1.8250.20061880.20083404
1.825-1.86470.20112100.18893426
1.8647-1.90810.20731890.18823478
1.9081-1.95580.181720.18493432
1.9558-2.00870.19311810.17843472
2.0087-2.06780.18462060.17713401
2.0678-2.13460.16821640.16963487
2.1346-2.21080.1931790.17333422
2.2108-2.29940.19052210.17283425
2.2994-2.4040.18881810.16873457
2.404-2.53080.19711630.16973487
2.5308-2.68940.18041620.16173439
2.6894-2.8970.19011780.16823461
2.897-3.18860.16231690.17223473
3.1886-3.650.16561760.16433450
3.65-4.59860.15011740.1363471
4.5986-94.2930.1641870.16763449
Refinement TLS params.Method: refined / Origin x: 3.0868 Å / Origin y: -40.3339 Å / Origin z: -4.9129 Å
111213212223313233
T0.1657 Å2-0.0217 Å2-0.0286 Å2-0.1577 Å20.0196 Å2--0.2878 Å2
L2.004 °2-0.6182 °20.9621 °2-0.611 °2-0.3997 °2--0.9902 °2
S0.0359 Å °-0.025 Å °-0.0215 Å °-0.0004 Å °-0.0117 Å °0.0091 Å °0.0054 Å °-0.0207 Å °-0.0264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA267 - 507
2X-RAY DIFFRACTION1allA601 - 801
3X-RAY DIFFRACTION1allS1 - 255

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