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- PDB-5ufo: Structure of RORgt bound to -

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Basic information

Entry
Database: PDB / ID: 5ufo
TitleStructure of RORgt bound to
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Nuclear Hormone Receptor
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-87J / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsSpurlino, J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Identification and structure activity relationships of quinoline tertiary alcohol modulators of ROR gamma t.
Authors: Kummer, D.A. / Cummings, M.D. / Abad, M. / Barbay, J. / Castro, G. / Wolin, R. / Kreutter, K.D. / Maharoof, U. / Milligan, C. / Nishimura, R. / Pierce, J. / Schalk-Hihi, C. / Spurlino, J. / ...Authors: Kummer, D.A. / Cummings, M.D. / Abad, M. / Barbay, J. / Castro, G. / Wolin, R. / Kreutter, K.D. / Maharoof, U. / Milligan, C. / Nishimura, R. / Pierce, J. / Schalk-Hihi, C. / Spurlino, J. / Urbanski, M. / Venkatesan, H. / Wang, A. / Woods, C. / Xue, X. / Edwards, J.P. / Fourie, A.M. / Leonard, K.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)30,7062
Polymers30,1031
Non-polymers6031
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.811, 88.811, 144.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 30102.688 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) / References: UniProt: P51449
#2: Chemical ChemComp-87J / (S)-{4-chloro-2-methoxy-3-[4-(methylsulfonyl)phenyl]quinolin-6-yl}(1-methyl-1H-imidazol-5-yl)[6-(trifluoromethyl)pyridin-3-yl]methanol


Mass: 603.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H22ClF3N4O4S

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.35M NaFormate, 0.1M Hepes pH7, 3%MPD

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→37.814 Å / Num. obs: 8782 / % possible obs: 99.82 % / Redundancy: 17.4 % / Net I/σ(I): 22.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→37.814 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2435 879 10.01 %
Rwork0.1907 --
obs0.196 8782 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→37.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 41 0 1881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031921
X-RAY DIFFRACTIONf_angle_d0.5822592
X-RAY DIFFRACTIONf_dihedral_angle_d13.155712
X-RAY DIFFRACTIONf_chiral_restr0.02278
X-RAY DIFFRACTIONf_plane_restr0.002339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8016-2.97710.30251420.23881275X-RAY DIFFRACTION99
2.9771-3.20680.31451420.23151283X-RAY DIFFRACTION100
3.2068-3.52930.27971440.21241288X-RAY DIFFRACTION100
3.5293-4.03950.24471450.17371304X-RAY DIFFRACTION100
4.0395-5.08740.19141470.16961322X-RAY DIFFRACTION100
5.0874-37.81740.23741590.18741431X-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)
17.911-0.29773.42862.5911-0.61072.682-0.25230.27120.742-0.1257-0.1473-0.1483-0.55830.11690.37190.4409-0.02160.0030.4249-0.02950.285824.3089-18.0733-1.2154
22.61430.79482.46270.97610.8282.35460.09041.58570.2487-0.22830.03960.186-0.03510.2665-0.1550.3899-0.0089-0.02850.50830.01480.393410.5696-25.7457-15.2568
36.5106-3.8837-1.45519.42492.59196.69990.17830.8015-0.1736-0.6326-0.0736-0.15160.52670.7887-0.05730.51740.1074-0.1080.68570.05010.330428.5623-31.4699-9.9532
45.38950.30642.17311.26460.08142.44690.1214-0.2771-0.27450.0675-0.06310.03950.26240.0001-0.08220.4701-0.01830.02350.31620.0660.246220.6515-30.4506-1.2129
54.2925-2.6362-2.95156.25370.4954.0013-0.1071-0.065-0.3463-0.4374-0.06760.54790.83710.15990.00060.54010.0823-0.05010.4957-0.01350.436823.5686-31.771510.5915
60.99440.61752.99160.39361.90789.1310.060.5865-0.0828-0.4166-0.79870.52450.770.3860.60351.43420.2861-0.09240.57030.04070.776113.5605-39.694-13.0544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 301 )
2X-RAY DIFFRACTION2chain 'A' and (resid 302 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 456 )
5X-RAY DIFFRACTION5chain 'A' and (resid 457 through 470 )
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 489 )

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