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- PDB-6b31: Structure of RORgt in complex with a novel inverse agonist 2 -

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Basic information

Entry
Database: PDB / ID: 6b31
TitleStructure of RORgt in complex with a novel inverse agonist 2
ComponentsNuclear receptor ROR-gamma
Keywordssignaling protein/agonist / Complex / inverse agonist / Nuclear Hormone Receptor / SIGNALING PROTEIN / signaling protein-agonist complex
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-CFJ / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.18 Å
AuthorsSkene, R.J. / Hoffman, I.
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Identification of novel quinazolinedione derivatives as ROR gamma t inverse agonist.
Authors: Fukase, Y. / Sato, A. / Tomata, Y. / Ochida, A. / Kono, M. / Yonemori, K. / Koga, K. / Okui, T. / Yamasaki, M. / Fujitani, Y. / Nakagawa, H. / Koyama, R. / Nakayama, M. / Skene, R. / Sang, B. ...Authors: Fukase, Y. / Sato, A. / Tomata, Y. / Ochida, A. / Kono, M. / Yonemori, K. / Koga, K. / Okui, T. / Yamasaki, M. / Fujitani, Y. / Nakagawa, H. / Koyama, R. / Nakayama, M. / Skene, R. / Sang, B.C. / Hoffman, I. / Shirai, J. / Yamamoto, S.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2244
Polymers53,2322
Non-polymers9922
Water27015
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1122
Polymers26,6161
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1122
Polymers26,6161
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.428, 96.428, 130.846
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 26615.830 Da / Num. of mol.: 2
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-CFJ / (3S)-N~1~-(3-chloro-4-cyanophenyl)-N~5~-(1,3-diethyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-6-yl)-3-methylpentanediamide


Mass: 495.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6M Sodium Formate, 3% MPD, and 100 mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 11664 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.085 / Χ2: 1.002 / Net I/σ(I): 9 / Num. measured all: 54865
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.18-3.234.70.6525710.9651100
3.23-3.294.80.5385811.0051100
3.29-3.364.80.4655660.9911100
3.36-3.434.80.3755881.011100
3.43-3.54.70.2765751.0531100
3.5-3.584.70.1835890.9311100
3.58-3.674.80.195711.0411100
3.67-3.774.70.1845891.031100
3.77-3.884.70.1465910.985199.8
3.88-4.014.70.1335731.05199.8
4.01-4.154.80.0955780.9711100
4.15-4.324.70.0965800.9941100
4.32-4.514.70.0955881.0011100
4.51-4.754.70.0865751.0021100
4.75-5.054.60.0895891.0181100
5.05-5.444.70.0845911.0261100
5.44-5.984.60.0815920.9771100
5.98-6.854.50.0685771.0011100
6.85-8.624.80.0375910.9951100
8.62-504.60.0296090.992199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.18→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.933 / SU B: 50.277 / SU ML: 0.377 / SU R Cruickshank DPI: 0.3616 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.466 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 555 4.8 %RANDOM
Rwork0.1608 ---
obs0.1649 11056 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 178.13 Å2 / Biso mean: 96.731 Å2 / Biso min: 57.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å2-0 Å2
2--1.72 Å2-0 Å2
3----5.58 Å2
Refinement stepCycle: final / Resolution: 3.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 70 15 3807
Biso mean--75.59 77.77 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193872
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9685213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12123.021192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4415710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1761534
X-RAY DIFFRACTIONr_chiral_restr0.0990.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022938
LS refinement shellResolution: 3.179→3.261 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 41 -
Rwork0.226 801 -
all-842 -
obs--99.41 %
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)
13.47132.25040.89643.50771.50242.9869-0.04650.1359-0.0386-0.00840.02520.1664-0.10570.11760.02130.11910.09390.02170.10260.0050.022136.833-2.1043.318
22.7296-1.6723-0.23164.17061.25922.396-0.1126-0.2014-0.00260.00260.07430.10290.08480.05440.03820.1038-0.0329-0.02140.07920.0240.013636.407-2.95-31.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A265 - 492
2X-RAY DIFFRACTION1A600
3X-RAY DIFFRACTION2B265 - 491
4X-RAY DIFFRACTION2B600

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