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- PDB-6nwt: RORgamma Ligand Binding Domain -

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Basic information

Entry
Database: PDB / ID: 6nwt
TitleRORgamma Ligand Binding Domain
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Orphan Nuclear Receptor / synthetic modulator / chemical probe
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-L7P / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0134
Polymers56,9582
Non-polymers1,0552
Water2,054114
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0062
Polymers28,4791
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0062
Polymers28,4791
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.590, 99.590, 129.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: 28478.979 Da / Num. of mol.: 2 / 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-L7P / 1,1,1,3,3,3-hexafluoro-2-[2-fluoro-4'-({4-[(pyridin-4-yl)methyl]piperazin-1-yl}methyl)[1,1'-biphenyl]-4-yl]propan-2-ol


Mass: 527.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24F7N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100-250 mM ammonium sulfate, 10-25% PEG3350, 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97741 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.35→28.75 Å / Num. obs: 30310 / % possible obs: 99.82 % / Redundancy: 2 % / Net I/σ(I): 21.07
Reflection shellResolution: 2.35→28.75 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QM0

4qm0


Resolution: 2.35→29.121 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1563 5.16 %
Rwork0.1806 --
obs0.1823 30294 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→29.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 74 114 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043951
X-RAY DIFFRACTIONf_angle_d0.6265329
X-RAY DIFFRACTIONf_dihedral_angle_d18.4262368
X-RAY DIFFRACTIONf_chiral_restr0.034572
X-RAY DIFFRACTIONf_plane_restr0.003673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3503-2.42610.24751430.20122614X-RAY DIFFRACTION100
2.4261-2.51280.23731510.2042589X-RAY DIFFRACTION100
2.5128-2.61330.26551140.2032632X-RAY DIFFRACTION100
2.6133-2.73220.26881280.20262616X-RAY DIFFRACTION100
2.7322-2.87610.24591280.19022621X-RAY DIFFRACTION100
2.8761-3.05610.23511650.19762577X-RAY DIFFRACTION100
3.0561-3.29180.23891490.20292613X-RAY DIFFRACTION100
3.2918-3.62250.25291680.18462590X-RAY DIFFRACTION100
3.6225-4.14540.17431190.16572637X-RAY DIFFRACTION100
4.1454-5.21790.19261310.15532619X-RAY DIFFRACTION99
5.2179-29.12340.17591670.17662623X-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)
13.30432.2165-1.58794.4474-0.53491.4134-0.1957-0.0152-0.322-0.0937-0.017-0.28610.16340.13720.18330.28860.03390.02740.28560.05070.2555-34.0652-1.831915.7613
22.10211.9194-1.89483.6418-1.22471.97560.0696-0.17960.06170.2589-0.22290.1067-0.0210.12040.14060.30110.02870.03540.34670.00580.2808-39.22850.504723.518
30.86920.8704-0.31491.5703-0.51021.1669-0.02740.55060.331-0.13230.13360.2314-0.17210.0940.01260.44330.11280.0490.76420.17390.5586-40.8126.176717.9485
43.1993-2.78773.5973.9906-2.33074.6683-0.4960.11881.50150.2375-0.7113-0.6211-0.79930.0920.91310.54690.027-0.19570.3820.0070.598-42.346112.3332-19.2475
52.995-3.21270.64576.5185-0.7970.5276-0.06170.16350.2490.2479-0.1622-0.6995-0.12330.2370.19730.3039-0.0184-0.04210.3540.05510.3369-26.0436-8.5499-9.7696
61.8746-1.58671.5482.0942-1.29351.65510.0930.0146-0.1049-0.0625-0.11140.0160.1013-0.07190.02830.2482-0.0409-0.0220.26830.03730.2554-40.4937-4.5782-17.0506
72.3596-0.72650.35491.00750.05082.3515-0.0237-0.7732-0.40740.28540.02310.32840.9748-0.3435-0.05360.7832-0.15430.0550.75150.1310.5371-42.9857-7.7946-13.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 368 )
2X-RAY DIFFRACTION2chain 'A' and (resid 369 through 456 )
3X-RAY DIFFRACTION3chain 'A' and (resid 457 through 497 )
4X-RAY DIFFRACTION4chain 'C' and (resid 265 through 284 )
5X-RAY DIFFRACTION5chain 'C' and (resid 285 through 337 )
6X-RAY DIFFRACTION6chain 'C' and (resid 338 through 456 )
7X-RAY DIFFRACTION7chain 'C' and (resid 457 through 509 )

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