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- PDB-7xqe: Crystal Structure of human RORgamma (C455E) LBD in complex with c... -

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Basic information

Entry
Database: PDB / ID: 7xqe
TitleCrystal Structure of human RORgamma (C455E) LBD in complex with compound XY039
ComponentsNuclear receptor ROR-gamma
KeywordsDNA BINDING PROTEIN / ROR gamma / LBD / Inhibitor
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 / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
Similarity search - Domain/homology
ETHANOL / Chem-H4I / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWu, X. / Li, C. / Zhang, Y. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81373325 China
CitationJournal: Acta Pharmacol.Sin. / Year: 2024
Title: Discovery and pharmacological characterization of 1,2,3,4-tetrahydroquinoline derivatives as ROR gamma inverse agonists against prostate cancer.
Authors: Wu, X.S. / Luo, X.Y. / Li, C.C. / Zhao, X.F. / Zhang, C. / Chen, X.S. / Lu, Z.F. / Wu, T. / Yu, H.N. / Peng, C. / Hu, Q.Q. / Shen, H. / Xu, Y. / Zhang, Y.
History
DepositionMay 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)63,6738
Polymers62,2582
Non-polymers1,4156
Water23413
1
A: Nuclear receptor ROR-gamma
hetero molecules

A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,81110
Polymers62,2582
Non-polymers1,5548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area2550 Å2
ΔGint-16 kcal/mol
Surface area20890 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules

B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5356
Polymers62,2582
Non-polymers1,2774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area1920 Å2
ΔGint-18 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.470, 83.470, 317.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 266 - 465 / Label seq-ID: 26 - 225

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 31128.926 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-H4I / 2,4-difluoro-N-(1-((4-(trifluoromethyl)benzyl)sulfonyl)-1,2,3,4-tetrahydroquinolin-7-yl)benzenesulfonamide


Mass: 546.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19F5N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M Tris pH 8.5, 16% v/v Ethanol, 4% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.57→80.72 Å / Num. obs: 18505 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.031 / Rrim(I) all: 0.088 / Net I/σ(I): 14.5 / Num. measured all: 151130 / Scaling rejects: 651
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.57-2.688.50.891886722220.8110.3230.9482.5
8.9-80.726.90.0436985350.9980.0160.04333.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0W

3b0w


Resolution: 2.57→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.725 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.576 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 915 5 %RANDOM
Rwork0.2268 ---
obs0.2293 17496 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.03 Å2 / Biso mean: 67.673 Å2 / Biso min: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å2-0 Å20 Å2
2--1.21 Å2-0 Å2
3----2.43 Å2
Refinement stepCycle: final / Resolution: 2.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 93 13 3455
Biso mean--69.1 49.35 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193508
X-RAY DIFFRACTIONr_bond_other_d0.0020.023239
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9764725
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0047479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9615408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81923.218174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9215639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5241530
X-RAY DIFFRACTIONr_chiral_restr0.0650.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
Refine LS restraints NCS

Ens-ID: 1 / Number: 12486 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.57→2.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 62 -
Rwork0.375 1253 -
all-1315 -
obs--99.92 %

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