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- PDB-5aph: Ligand complex of RORg LBD -

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Basic information

Entry
Database: PDB / ID: 5aph
TitleLigand complex of RORg LBD
Components
  • NUCLEAR RECEPTOR COACTIVATOR 2
  • NUCLEAR RECEPTOR ROR-GAMMA
KeywordsTRANSCRIPTION / RORG LIGAND / RORG AGONIST / STRUCTURE-BASED DESIGN
Function / homology
Function and homology information


tolerance induction in gut-associated lymphoid tissue / regulation of steroid metabolic process / cellular response to sterol / Peyer's patch development / ligand-modulated transcription factor activity / positive regulation of circadian rhythm / regulatory T cell differentiation / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding ...tolerance induction in gut-associated lymphoid tissue / regulation of steroid metabolic process / cellular response to sterol / Peyer's patch development / ligand-modulated transcription factor activity / positive regulation of circadian rhythm / regulatory T cell differentiation / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / lymph node development / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / T-helper 17 cell differentiation / adipose tissue development / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / transcription regulator inhibitor activity / cellular response to hormone stimulus / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / positive regulation of adipose tissue development / bile acid and bile salt transport / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / negative regulation of smoothened signaling pathway / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA-binding transcription repressor activity, RNA polymerase II-specific / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coregulator activity / sequence-specific double-stranded DNA binding / rhythmic process / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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-VYI / Nuclear receptor coactivator 2 / Nuclear receptor ROR-gamma / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsXue, Y. / Aagaard, A. / Narjes, F.
CitationJournal: ChemMedChem / Year: 2016
Title: Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor ROR gamma.
Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. ...Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. / Hansson, T.G. / Narjes, F.
History
DepositionSep 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR RECEPTOR ROR-GAMMA
C: NUCLEAR RECEPTOR COACTIVATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8894
Polymers32,3942
Non-polymers4952
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-2.5 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.850, 61.850, 159.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 / RORG


Mass: 30901.402 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 265-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51449
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 2


Mass: 1492.788 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 686-697
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E7EWM1, UniProt: Q15596*PLUS
#3: Chemical ChemComp-VYI / N-(2-FLUOROPHENYL)-4-[(4-FLUOROPHENYL)SULFONYL]-2,3,4,5-TETRAHYDRO-1,4-BENZOXAZEPIN-6-AMINE


Mass: 416.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F2N2O3S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-(2-FLUOROPHENYL)-4-[(4-FLUOROPHENYL)SULFONYL]-2,3,4, 5-TETRAHYDRO-1,4-BENZOXAZEPIN-6-AMINE (VYI): ...N-(2-FLUOROPHENYL)-4-[(4-FLUOROPHENYL)SULFONYL]-2,3,4, 5-TETRAHYDRO-1,4-BENZOXAZEPIN-6-AMINE (VYI): COMPOUND STRCTURE IN THE ATTACHED PICTURE FILE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.54→48.82 Å / Num. obs: 43870 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 30.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.3 / % possible all: 65.8

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L0L

3l0l


Resolution: 1.54→48.82 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.9268 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 2193 5 %RANDOM
Rwork0.2125 ---
obs0.2139 43827 93.98 %-
Displacement parametersBiso mean: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.9581 Å20 Å20 Å2
2---2.9581 Å20 Å2
3---5.9162 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.54→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 33 297 2489
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943051HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d811SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2264HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion16.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion273SEMIHARMONIC5
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_contact2895SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2903 108 5.12 %
Rwork0.2638 2003 -
all0.265 2111 -
obs--93.98 %

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