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- PDB-6nwu: RORgamma Ligand Binding Domain -

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Basic information

Entry
Database: PDB / ID: 6nwu
TitleRORgamma Ligand Binding Domain
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Orphan Nuclear Receptor / synthetic modulator / chemical probe
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-L7J / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStrutzenberg, T.S. / Park, H. / Griffin, P.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA206493 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM126842 United States
CitationJournal: Elife / Year: 2019
Title: HDX-MS reveals structural determinants for ROR gamma hyperactivation by synthetic agonists.
Authors: Strutzenberg, T.S. / Garcia-Ordonez, R.D. / Novick, S.J. / Park, H. / Chang, M.R. / Doebellin, C. / He, Y. / Patouret, R. / Kamenecka, T.M. / Griffin, P.R.
History
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5862
Polymers30,0831
Non-polymers5031
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 59.880, 162.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 30082.859 Da / Num. of mol.: 1 / Fragment: ligand binding domain (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) / References: UniProt: P51449
#2: Chemical ChemComp-L7J / 6-[(3,5-dichloropyridin-4-yl)methoxy]-1-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3-dihydro-1H-indole


Mass: 503.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15Cl2F3N2O3S / Feature type: SUBJECT OF INVESTIGATION

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M sodium phosphate, pH 7.4, 0.5-0.7 M sodium chloride, 4-6% PEG4000, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→56.19 Å / Num. obs: 5345 / % possible obs: 99.96 % / Redundancy: 11.6 % / Net I/σ(I): 9.55
Reflection shellResolution: 3.2→3.3 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VB3

5vb3


Resolution: 3.2→56.189 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.276 535 10.01 %
Rwork0.2176 --
obs0.2237 5343 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→56.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 32 0 2131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032189
X-RAY DIFFRACTIONf_angle_d0.6772956
X-RAY DIFFRACTIONf_dihedral_angle_d8.2811822
X-RAY DIFFRACTIONf_chiral_restr0.038318
X-RAY DIFFRACTIONf_plane_restr0.003376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.52220.31971310.26131173X-RAY DIFFRACTION100
3.5222-4.03170.34321290.22261164X-RAY DIFFRACTION100
4.0317-5.0790.28661310.18771186X-RAY DIFFRACTION100
5.079-56.19740.21041440.21921285X-RAY DIFFRACTION100
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)
12.7266-1.71012.21813.5083-3.1025.5055-0.1994-0.15530.6141-0.5282-0.7061-1.07690.84471.06780.30780.28050.11760.1640.722-0.19020.494216.338413.81828.7345
21.8997-1.03211.21694.76411.41132.159-0.03280.03831.2352-0.4677-0.1936-0.5823-0.4620.73650.34850.5616-0.14380.1440.4770.18220.6227-0.892234.607411.7192
31.2251-1.33540.73563.419-1.7392.88080.12590.13980.2092-0.5127-0.1333-0.45380.22790.28750.00870.3248-0.0720.1140.28440.0190.3595-3.037621.006617.0461
42.0358-1.60880.8382.6342-0.01741.8632-0.0402-0.19910.29130.05830.1441-0.23180.14620.3497-0.05460.3505-0.05660.04950.4567-0.00680.31382.671818.149632.3764
53.56180.0334-0.26185.45350.86255.52990.2738-0.02870.0133-0.1684-0.07910.64240.1655-0.6032-0.37740.3504-0.0196-0.00230.33930.07650.4302-14.895716.631216.0311
68.9427-3.9037-2.69978.72861.51047.6375-0.20091.2702-1.885-0.34450.10770.291.46820.14310.2340.97590.17110.01070.5171-0.13790.5183-3.62544.670111.6363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 312 )
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 468 )
5X-RAY DIFFRACTION5chain 'A' and (resid 469 through 506 )
6X-RAY DIFFRACTION6chain 'A' and (resid 507 through 523 )

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