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- PDB-6b30: Structure of RORgt in complex with a novel inverse agonist 1 -

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Basic information

Entry
Database: PDB / ID: 6b30
TitleStructure of RORgt in complex with a novel inverse agonist 1
ComponentsNuclear receptor ROR-gamma
KeywordsSIGNALING PROTEIN / Complex / inverse agonist / 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-CFG / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsSkene, R.J. / Hoffman, I.
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Discovery of orally efficacious ROR gamma t inverse agonists, part 1: Identification of novel phenylglycinamides as lead scaffolds.
Authors: Shirai, J. / Tomata, Y. / Kono, M. / Ochida, A. / Fukase, Y. / Sato, A. / Masada, S. / Kawamoto, T. / Yonemori, K. / Koyama, R. / Nakagawa, H. / Nakayama, M. / Uga, K. / Shibata, A. / Koga, ...Authors: Shirai, J. / Tomata, Y. / Kono, M. / Ochida, A. / Fukase, Y. / Sato, A. / Masada, S. / Kawamoto, T. / Yonemori, K. / Koyama, R. / Nakagawa, H. / Nakayama, M. / Uga, K. / Shibata, A. / Koga, K. / Okui, T. / Shirasaki, M. / Skene, R. / Sang, B. / Hoffman, I. / Lane, W. / Fujitani, Y. / Yamasaki, M. / Yamamoto, S.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 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)50,9094
Polymers50,0022
Non-polymers9072
Water84747
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4542
Polymers25,0011
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4542
Polymers25,0011
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.217, 97.217, 131.561
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: 25000.916 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-CFG / N-[(1R)-1-(4-methoxyphenyl)-2-oxo-2-{[4-(trimethylsilyl)phenyl]amino}ethyl]-N-methyl-3-oxo-2,3-dihydro-1,2-oxazole-5-carboxamide


Mass: 453.563 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N3O5Si
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.59 Å3/Da / Density % sol: 65.73 %
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: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 19499 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.078 / Χ2: 1.001 / Net I/σ(I): 11 / Num. measured all: 135322
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.69-2.7470.8599700.979199.7
2.74-2.7970.7539660.985199.1
2.79-2.8470.6659600.993199.6
2.84-2.970.5039810.989199.7
2.9-2.9670.4569761.013199.6
2.96-3.0370.3679721.023199.7
3.03-3.1170.319751.0311100
3.11-3.197.10.2719691199.7
3.19-3.286.90.1969971.014199.8
3.28-3.3970.1619620.9821100
3.39-3.5170.1359810.995199.8
3.51-3.6570.0959771.003199.8
3.65-3.8270.0799670.988199.5
3.82-4.026.90.0679861.008199.3
4.02-4.276.90.0599691.007199.6
4.27-4.66.90.0599790.999199.2
4.6-5.066.70.0599821.008199.6
5.06-5.796.70.0669801.028199.2
5.79-7.296.70.0519641.004197.7
7.29-5070.0329860.978196.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 24.164 / SU ML: 0.229 / SU R Cruickshank DPI: 0.485 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.284
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 991 5.1 %RANDOM
Rwork0.1891 ---
obs0.1914 18452 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.8 Å2 / Biso mean: 76.11 Å2 / Biso min: 46.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å2-0 Å2
2--0.74 Å20 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 64 47 3586
Biso mean--68.17 69.01 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193610
X-RAY DIFFRACTIONr_bond_other_d0.0010.023428
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9724859
X-RAY DIFFRACTIONr_angle_other_deg0.90237856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9675425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57923.011176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15215666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4661532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
LS refinement shellResolution: 2.689→2.759 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 74 -
Rwork0.259 1322 -
all-1396 -
obs--97.21 %
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)
12.8436-0.5893-1.63560.22710.27961.4785-0.02520.1031-0.0192-0.0441-0.0286-0.08350.1613-0.23230.05380.1007-0.06450.03960.13520.01610.0741-17.78132.7883.475
20.85710.5535-0.22431.6121-1.00740.8797-0.0573-0.0127-0.01780.0473-0.0297-0.0560.03690.15440.0870.1264-0.02690.03590.14250.0110.0264-14.83233.962-33.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A265 - 479
2X-RAY DIFFRACTION1A600
3X-RAY DIFFRACTION2B265 - 476
4X-RAY DIFFRACTION2B600

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