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- PDB-4ypq: Crystal structure of the ROR(gamma)t ligand binding domain in com... -

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Basic information

Entry
Database: PDB / ID: 4ypq
TitleCrystal structure of the ROR(gamma)t ligand binding domain in complex with 4-(1-(2-chloro-6-(trifluoromethyl)benzoyl)-1H-indazol-3-yl)benzoic acid
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / nuclear receptor ligand binding domain
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 / Retinoid X Receptor / Retinoid X Receptor / 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 receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4F1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLeysen, S. / Scheepstra, M. / van Almen, G.C. / Ottmann, C. / Brunsveld, L.
CitationJournal: Nat Commun / Year: 2015
Title: Identification of an allosteric binding site for ROR gamma t inhibition.
Authors: Scheepstra, M. / Leysen, S. / van Almen, G.C. / Miller, J.R. / Piesvaux, J. / Kutilek, V. / van Eenennaam, H. / Zhang, H. / Barr, K. / Nagpal, S. / Soisson, S.M. / Kornienko, M. / Wiley, K. ...Authors: Scheepstra, M. / Leysen, S. / van Almen, G.C. / Miller, J.R. / Piesvaux, J. / Kutilek, V. / van Eenennaam, H. / Zhang, H. / Barr, K. / Nagpal, S. / Soisson, S.M. / Kornienko, M. / Wiley, K. / Elsen, N. / Sharma, S. / Correll, C.C. / Trotter, B.W. / van der Stelt, M. / Oubrie, A. / Ottmann, C. / Parthasarathy, G. / Brunsveld, L.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,7773
Polymers28,3081
Non-polymers4692
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.809, 173.809, 67.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-602-

MG

21A-757-

HOH

31A-786-

HOH

41A-787-

HOH

51A-801-

HOH

61A-811-

HOH

71A-823-

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: 28307.824 Da / Num. of mol.: 1 / Fragment: UNP residues 265-507
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) / Strain (production host): Nico321(DE3) / References: UniProt: P51449
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1M Tris pH 8.5, 7% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.5 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.32→35.47 Å / Num. obs: 16884 / % possible obs: 100 % / Redundancy: 11.7 % / Rsym value: 0.121 / Net I/σ(I): 12.1
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.886 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
Aimlessdata scaling
Cootmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NIE

4nie


Resolution: 2.32→35.465 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 841 4.98 %
Rwork0.1751 --
obs0.1778 16882 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→35.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 32 130 2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082065
X-RAY DIFFRACTIONf_angle_d1.0632786
X-RAY DIFFRACTIONf_dihedral_angle_d14.837788
X-RAY DIFFRACTIONf_chiral_restr0.042301
X-RAY DIFFRACTIONf_plane_restr0.004384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3201-2.46540.30431390.22242646X-RAY DIFFRACTION100
2.4654-2.65570.29671360.2122645X-RAY DIFFRACTION100
2.6557-2.92280.26641380.19312672X-RAY DIFFRACTION100
2.9228-3.34550.25261340.18812663X-RAY DIFFRACTION100
3.3455-4.21390.20161540.15762671X-RAY DIFFRACTION100
4.2139-35.46880.2061400.16142744X-RAY DIFFRACTION100

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