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- PDB-5ejv: RORy in complex with T090131718 and Coactivator peptide EBI96 -

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Basic information

Entry
Database: PDB / ID: 5ejv
TitleRORy in complex with T090131718 and Coactivator peptide EBI96
Components
  • EBI96 Coactivator Peptide
  • Nuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / RORgamma / T090131718 / Coactivator peptide
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / Retinoid X Receptor / Retinoid X Receptor / 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 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-444 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMarcotte, D.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Discovery of biaryls as ROR gamma inverse agonists by using structure-based design.
Authors: Enyedy, I.J. / Powell, N.A. / Caravella, J. / van Vloten, K. / Chao, J. / Banerjee, D. / Marcotte, D. / Silvian, L. / McKenzie, A. / Hong, V.S. / Fontenot, J.D.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
C: EBI96 Coactivator Peptide
B: Nuclear receptor ROR-gamma
D: EBI96 Coactivator Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6736
Polymers64,7114
Non-polymers9632
Water57632
1
A: Nuclear receptor ROR-gamma
C: EBI96 Coactivator Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8373
Polymers32,3552
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-16 kcal/mol
Surface area12810 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
D: EBI96 Coactivator Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8373
Polymers32,3552
Non-polymers4811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.139, 63.139, 160.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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: 30250.900 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain (UNP residues 259-518)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51449
#2: Protein/peptide EBI96 Coactivator Peptide


Mass: 2104.355 Da / Num. of mol.: 2 / Fragment: Coactivator Peptide / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-444 / N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE


Mass: 481.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12F9NO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0M Na Acetate/0.2M NaSCN/0.1M TRIS pH 7.0 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.58→63.14 Å / Num. obs: 19787 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/av σ(I): 4.875 / Net I/σ(I): 8.8 / Num. measured all: 147183
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
2.58-2.727.40.9120.82151628910.9122.6100
2.72-2.887.40.5921.32045627460.5923.8100
2.88-3.087.50.37321896825400.3735.5100
3.08-3.337.50.2263.31790423960.2267.7100
3.33-3.657.50.1365.41630921790.13610.6100
3.65-4.087.50.0887.91495619960.08813100
4.08-4.717.50.087.91310917490.0814.7100
4.71-5.777.50.1035.81115614940.10315100
5.77-8.167.50.0778858111510.07715.2100
8.16-63.146.60.04413.642286450.04415.299

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0L

3l0l


Resolution: 2.58→63.14 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.848 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.739 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 968 4.9 %RANDOM
Rwork0.1793 ---
obs0.182 18768 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.91 Å2 / Biso mean: 46.393 Å2 / Biso min: 22.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.58→63.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4163 0 62 32 4257
Biso mean--112.86 44.71 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194322
X-RAY DIFFRACTIONr_bond_other_d0.0020.024131
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.9735846
X-RAY DIFFRACTIONr_angle_other_deg1.15239457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67122.995207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18115765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8431534
X-RAY DIFFRACTIONr_chiral_restr0.1330.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021077
X-RAY DIFFRACTIONr_mcbond_it2.7133.8472048
X-RAY DIFFRACTIONr_mcbond_other2.7093.8462047
X-RAY DIFFRACTIONr_mcangle_it4.1335.7662553
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 62 -
Rwork0.223 1397 -
all-1459 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3802-0.24390.14160.40890.11040.53770.00830.0185-0.0271-0.0050.03910.04920.00490.0466-0.04740.0086-0.00080.00340.01130.00470.02210.597862.8275-20.3193
21.4183-2.12520.77453.56370.35576.5141-0.0066-0.01550.0810.00980.0494-0.1472-0.03930.0439-0.04280.04070.0609-0.01760.0993-0.01630.037626.018259.5553-10.1587
30.2267-0.30550.04431.12970.6090.8032-0.02960.0104-0.0230.06010.00480.06260.02030.0540.02480.00870.00690.01320.01770.01430.02540.990791.6913-27.2662
40.6554-2.5820.193510.3806-0.77680.1065-0.107-0.06780.0030.15450.24610.01440.01710.0061-0.13910.12110.0255-0.08180.0698-0.05620.234555.788485.2317-18.2785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A263 - 507
2X-RAY DIFFRACTION2C1 - 11
3X-RAY DIFFRACTION3B264 - 508
4X-RAY DIFFRACTION4D2 - 13

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