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- PDB-4nie: Crystal structure of the orphan nuclear receptor ROR(gamma)t liga... -

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Basic information

Entry
Database: PDB / ID: 4nie
TitleCrystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with small molecule ligand
Components
  • Nuclear receptor ROR-gamma
  • Peptide from Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION/AGONIST / nuclear receptor / ligand binding domain / TRANSCRIPTION-AGONIST complex
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
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / Chem-NBH / Nuclear receptor coactivator 2 / Nuclear receptor ROR-gamma / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMa, Y.L. / Yang, L.Q.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Discovery of Tertiary Amine and Indole Derivatives as Potent ROR gamma t Inverse Agonists.
Authors: Yang, T. / Liu, Q. / Cheng, Y. / Cai, W. / Ma, Y. / Yang, L. / Wu, Q. / Orband-Miller, L.A. / Zhou, L. / Xiang, Z. / Huxdorf, M. / Zhang, W. / Zhang, J. / Xiang, J.N. / Leung, S. / Qiu, Y. / ...Authors: Yang, T. / Liu, Q. / Cheng, Y. / Cai, W. / Ma, Y. / Yang, L. / Wu, Q. / Orband-Miller, L.A. / Zhou, L. / Xiang, Z. / Huxdorf, M. / Zhang, W. / Zhang, J. / Xiang, J.N. / Leung, S. / Qiu, Y. / Zhong, Z. / Elliott, J.D. / Lin, X. / Wang, Y.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
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.year / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
C: Peptide from Nuclear receptor coactivator 2
D: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6848
Polymers64,2414
Non-polymers1,4444
Water3,405189
1
A: Nuclear receptor ROR-gamma
D: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8424
Polymers32,1202
Non-polymers7222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-9 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
C: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8424
Polymers32,1202
Non-polymers7222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.085, 86.349, 91.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / Retinoid-related ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / Retinoid-related orphan receptor-gamma


Mass: 30627.467 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 263-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1F3, RORC, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449
#2: Protein/peptide Peptide from Nuclear receptor coactivator 2


Mass: 1492.788 Da / Num. of mol.: 2 / Fragment: UNP residues 684-697 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: E7EWM1, UniProt: Q15596*PLUS
#3: Chemical ChemComp-NBH / N-(4-{[benzyl(propyl)amino]methyl}phenyl)-2-[4-(ethylsulfonyl)phenyl]acetamide


Mass: 464.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32N2O3S
#4: Chemical ChemComp-DMX / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 257.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris, pH 6.5, 14% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→91.98 Å / Num. all: 36351 / Num. obs: 36335 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.2 / Num. unique all: 35890 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.028 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.219 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24677 1812 5 %RANDOM
Rwork0.20751 ---
obs0.20946 34458 99.72 %-
all-36371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.347 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-0 Å2
2---1.69 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.01→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 98 189 4382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194350
X-RAY DIFFRACTIONr_bond_other_d0.0010.024170
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9715880
X-RAY DIFFRACTIONr_angle_other_deg1.13939543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3225519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55523.284204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71515758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.071529
X-RAY DIFFRACTIONr_chiral_restr0.0540.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021096
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.220.3172058
X-RAY DIFFRACTIONr_mcbond_other0.220.3172057
X-RAY DIFFRACTIONr_mcangle_it0.3840.4732574
X-RAY DIFFRACTIONr_mcangle_other0.3840.4732575
X-RAY DIFFRACTIONr_scbond_it0.4110.5172292
X-RAY DIFFRACTIONr_scbond_other0.4110.5192293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6460.7443304
X-RAY DIFFRACTIONr_long_range_B_refined6.0283.6395125
X-RAY DIFFRACTIONr_long_range_B_other6.0273.6485126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.008→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 124 -
Rwork0.263 2490 -
obs--99.28 %
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)
11.04420.15440.17211.9769-0.33341.1916-0.0610.0307-0.04170.08350.0432-0.0572-0.03130.03510.01780.1990.01510.00560.22150.01390.15718.607-13.956-8.39
21.12881.16890.27095.54721.09910.9838-0.12030.0640.1649-0.00860.18310.094-0.18070.0369-0.06280.25540.0086-0.01790.2490.030.180115.66320.432-17.795
342.392829.97666.135126.95383.606423.4563-0.1619-0.4776-0.45550.6522-1.0842.1097-1.1881-0.44431.24590.30860.01420.32920.163-0.29721.19133.09215.462-4.25
416.3692-2.7946-2.440514.76035.775831.02640.2980.33810.62640.0641-0.20980.6682-0.3792-1.0745-0.08820.1816-0.00220.00680.29450.10850.43740.21-8.819-12.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A264 - 508
2X-RAY DIFFRACTION2B264 - 508
3X-RAY DIFFRACTION3C687 - 695
4X-RAY DIFFRACTION4D687 - 696

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