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- PDB-6o98: Crystal structure of RAR-related orphan receptor C in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6o98
TitleCrystal structure of RAR-related orphan receptor C in complex with a phenyl (3-phenylpyrrolidin-3-yl)sulfone inhibitor
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION/INHIBITOR / RORgt / nuclear hormone receptor / ligand-binding domain / inverse agonist / TRANSCRIPTION-INHIBITOR complex
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-L8A / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSack, J.S.
CitationJournal: ACS Med Chem Lett / Year: 2019
Title: Structure-based Discovery of Phenyl (3-Phenylpyrrolidin-3-yl)sulfones as Selective, Orally Active ROR gamma t Inverse Agonists.
Authors: Duan, J.J. / Lu, Z. / Jiang, B. / Stachura, S. / Weigelt, C.A. / Sack, J.S. / Khan, J. / Ruzanov, M. / Galella, M.A. / Wu, D.R. / Yarde, M. / Shen, D.R. / Shuster, D.J. / Borowski, V. / Xie, ...Authors: Duan, J.J. / Lu, Z. / Jiang, B. / Stachura, S. / Weigelt, C.A. / Sack, J.S. / Khan, J. / Ruzanov, M. / Galella, M.A. / Wu, D.R. / Yarde, M. / Shen, D.R. / Shuster, D.J. / Borowski, V. / Xie, J.H. / Zhang, L. / Vanteru, S. / Gupta, A.K. / Mathur, A. / Zhao, Q. / Foster, W. / Salter-Cid, L.M. / Carter, P.H. / Dhar, T.G.M.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMar 20, 2019ID: 6NXH
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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

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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)62,6744
Polymers61,4232
Non-polymers1,2512
Water905
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3372
Polymers30,7111
Non-polymers6261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3372
Polymers30,7111
Non-polymers6261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.780, 97.780, 126.280
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: 30711.455 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 265-508)
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-L8A / 1-(4-{(3R)-3-[(4-fluorophenyl)sulfonyl]-3-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]pyrrolidine-1-carbonyl}piperazin-1-yl)ethan-1-one


Mass: 625.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26F7N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growMethod: vapor diffusion, hanging drop / Details: unspecified

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→84.69 Å / Num. obs: 27744 / % possible obs: 95.5 % / Redundancy: 9.9 % / Biso Wilson estimate: 71.57 Å2 / Rmerge(I) obs: 0.176 / Rsym value: 0.176 / Net I/σ(I): 7.3
Reflection shellResolution: 2.29→2.39 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1387 / CC1/2: 0.469 / % possible all: 58.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BN6

6bn6


Resolution: 2.29→70.33 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.238
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1393 5.02 %RANDOM
Rwork0.246 ---
obs0.248 27743 89.5 %-
Displacement parametersBiso mean: 67.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.5881 Å20 Å20 Å2
2--0.5881 Å20 Å2
3----1.1762 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.29→70.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 84 5 3705
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083776HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15104HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1382SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes670HARMONIC5
X-RAY DIFFRACTIONt_it3776HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion464SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4472SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2078 -4.32 %
Rwork0.1817 531 -
all0.1828 555 -
obs--21.36 %

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