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- PDB-5iz0: RORgamma in complex with agonist BIO592 and Coactivator EBI96 -

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Basic information

Entry
Database: PDB / ID: 5iz0
TitleRORgamma in complex with agonist BIO592 and Coactivator EBI96
Components
  • GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
  • Nuclear receptor ROR-gamma
KeywordsIMMUNE SYSTEM / RORgamma / Nuclear hormone receptor / Agonist / AF2 helix
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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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-6F1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.635 Å
AuthorsMarcotte, D.J.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.
Authors: Marcotte, D.J. / Liu, Y. / Little, K. / Jones, J.H. / Powell, N.A. / Wildes, C.P. / Silvian, L.F. / Chodaparambil, J.V.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
B: Nuclear receptor ROR-gamma
E: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
D: Nuclear receptor ROR-gamma
F: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
G: Nuclear receptor ROR-gamma
H: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,76135
Polymers128,1768
Non-polymers2,58527
Water2,702150
1
A: Nuclear receptor ROR-gamma
C: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,77011
Polymers32,0442
Non-polymers7269
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-80 kcal/mol
Surface area12440 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
E: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6999
Polymers32,0442
Non-polymers6557
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-55 kcal/mol
Surface area12840 Å2
MethodPISA
3
D: Nuclear receptor ROR-gamma
F: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6287
Polymers32,0442
Non-polymers5845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-55 kcal/mol
Surface area12430 Å2
MethodPISA
4
G: Nuclear receptor ROR-gamma
H: GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6648
Polymers32,0442
Non-polymers6206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-64 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.672, 68.111, 96.056
Angle α, β, γ (deg.)90.000, 109.900, 90.000
Int Tables number4
Space group name H-MP1211

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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: 30352.002 Da / Num. of mol.: 4 / Fragment: Ligand Binding Domain
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): BL21(DE3) / References: UniProt: P51449
#2: Protein/peptide
GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN


Mass: 1691.918 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-6F1 / N-(4-ethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide


Mass: 442.452 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H21F3N2O4S
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M HEPES pH 8.0 0.2M NaCl 25% PEG3350

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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: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.635→80.558 Å / Num. obs: 31077 / % possible obs: 99.6 % / Redundancy: 2.63 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LOL

3lol
PDB Unreleased entry


Resolution: 2.635→80.558 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.388 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1557 5 %RANDOM
Rwork0.1994 ---
obs0.2023 29379 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.4 Å2 / Biso mean: 33.787 Å2 / Biso min: 3.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.635→80.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8239 0 143 150 8532
Biso mean--38.98 28.64 -
Num. residues----1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198542
X-RAY DIFFRACTIONr_bond_other_d0.0030.028202
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.97211539
X-RAY DIFFRACTIONr_angle_other_deg1.0993.00318785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09623.113408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.455151516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3231565
X-RAY DIFFRACTIONr_chiral_restr0.1160.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022107
X-RAY DIFFRACTIONr_mcbond_it1.9063.2694067
X-RAY DIFFRACTIONr_mcbond_other1.9053.2684058
X-RAY DIFFRACTIONr_mcangle_it3.0774.8995063
LS refinement shellResolution: 2.635→2.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 117 -
Rwork0.275 2157 -
all-2274 -
obs--99.61 %

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