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- PDB-6t4j: ROR(gamma)t ligand binding domain in complex with desmosterol and... -

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Basic information

Entry
Database: PDB / ID: 6t4j
TitleROR(gamma)t ligand binding domain in complex with desmosterol 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 / T-helper cell differentiation / positive regulation of circadian rhythm / 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 / T-helper cell differentiation / positive regulation of circadian rhythm / 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-L3E / desmosterol / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 14, 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)31,4514
Polymers30,5141
Non-polymers9373
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area12100 Å2
Unit cell
Length a, b, c (Å)108.910, 108.910, 98.483
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-784-

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-MHQ / desmosterol


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O / 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.: 186 / 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: 1.2M 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: 1.78→94.28 Å / Num. obs: 61587 / % possible obs: 100 % / Redundancy: 78 % / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.012 / Rrim(I) all: 0.107 / Net I/σ(I): 31.9
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.78-1.8116170.8021
1.78-94.28188911

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Processing

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

6sal


Resolution: 1.79→68.118 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 3110 5.05 %
Rwork0.1747 58477 -
obs0.1758 61587 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.63 Å2 / Biso mean: 37.4906 Å2 / Biso min: 19.79 Å2
Refinement stepCycle: final / Resolution: 1.79→68.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 66 186 2228
Biso mean--32.77 48.35 -
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
1.79-1.8180.32571450.31032656
1.818-1.84780.29831340.29072649
1.8478-1.87970.28591530.28342639
1.8797-1.91390.33331320.25912654
1.9139-1.95070.30181290.24162691
1.9507-1.99050.24581140.21372669
1.9905-2.03380.22621490.19612660
2.0338-2.08110.25031370.19442656
2.0811-2.13310.21451760.18832639
2.1331-2.19080.2231240.17892685
2.1908-2.25530.19761310.17932661
2.2553-2.32810.20941420.18122659
2.3281-2.41130.24781520.17682643
2.4113-2.50780.21611430.17562645
2.5078-2.6220.20481300.16892694
2.622-2.76020.18391500.16882632
2.7602-2.93320.18781330.17492672
2.9332-3.15960.21561250.18462660
3.1596-3.47760.19721940.1722613
3.4776-3.98070.15611320.15072662
3.9807-5.01510.13791460.13742665
5.0151-68.1180.2051390.17642673
Refinement TLS params.Method: refined / Origin x: 3.1032 Å / Origin y: -40.3597 Å / Origin z: -4.8943 Å
111213212223313233
T0.2322 Å2-0.0279 Å2-0.0431 Å2-0.2268 Å20.0318 Å2--0.2379 Å2
L2.1651 °2-0.8271 °20.9337 °2-0.8515 °2-0.5603 °2--1.0717 °2
S0.0537 Å °0.0329 Å °-0.0632 Å °-0.0089 Å °-0.0442 Å °0.009 Å °0.0089 Å °-0.0351 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA267 - 507
2X-RAY DIFFRACTION1allA601 - 801
3X-RAY DIFFRACTION1allS1 - 186

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