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- PDB-9kne: Crystal structure of human ERRg LBD in complex with 5-nitroindole -

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Basic information

Entry
Database: PDB / ID: 9kne
TitleCrystal structure of human ERRg LBD in complex with 5-nitroindole
Components
  • Estrogen-related receptor gamma
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / EsRRG / LBD / nuclear receptor / complex structure
Function / homology
Function and homology information


ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear steroid receptor activity / histone deacetylase complex / estrogen response element binding / nuclear retinoid X receptor binding ...ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear steroid receptor activity / histone deacetylase complex / estrogen response element binding / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / steroid binding / SUMOylation of transcription cofactors / nuclear estrogen receptor binding / nuclear receptor binding / cellular response to estradiol stimulus / circadian regulation of gene expression / Heme signaling / circadian rhythm / Nuclear Receptor transcription pathway / histone deacetylase binding / fibrillar center / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / transcription corepressor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Oestrogen-related receptor ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Oestrogen-related receptor / Retinoic acid receptor / Estrogen receptor/oestrogen-related receptor / : / 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
Similarity search - Domain/homology
5-nitro-1H-indole / R-1,2-PROPANEDIOL / Nuclear receptor-interacting protein 1 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, T. / Wang, N. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharmacol.Sin. / Year: 2025
Title: Identification of indoles as potential endogenous ligands of ERR gamma and their modulation on drug binding.
Authors: Shuai, Y.Y. / Zhang, H.Y. / Chen, R. / Wang, B.L. / Ding, P. / Dong, Y. / Sun, M.Z. / Wu, X.S. / Xu, Y. / Zhang, Y. / Liu, J.S. / Wang, N. / Xu, T.T.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 10, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
B: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5467
Polymers30,0802
Non-polymers4675
Water3,099172
1
A: Estrogen-related receptor gamma
B: Nuclear receptor-interacting protein 1
hetero molecules

A: Estrogen-related receptor gamma
B: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09314
Polymers60,1604
Non-polymers93310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area5860 Å2
ΔGint-12 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.095, 64.095, 137.526
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 Estrogen-related receptor gamma / ERR gamma-2 / Estrogen receptor-related protein 3 / Nuclear receptor subfamily 3 group B member 3


Mass: 28386.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62508
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 1692.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P48552
#3: Chemical ChemComp-2HU / 5-nitro-1H-indole


Mass: 162.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N2O2
#4: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30%(w/v) PEG 5000 MME 0.1M Tris 8.0 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→68.76 Å / Num. obs: 23843 / % possible obs: 86.8 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.015 / Rrim(I) all: 0.072 / Χ2: 0.91 / Net I/σ(I): 27.8 / Num. measured all: 502415
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 49.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.486 / Num. measured all: 7213 / Num. unique obs: 789 / CC1/2: 0.935 / Rpim(I) all: 0.164 / Rrim(I) all: 0.515 / Χ2: 0.68 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→58.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.557 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22407 1196 5 %RANDOM
Rwork0.17319 ---
obs0.1756 22585 86.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.908 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.8→58.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 32 172 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171896
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6292651
X-RAY DIFFRACTIONr_angle_other_deg1.4461.5774418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22425.16989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.104155
X-RAY DIFFRACTIONr_chiral_restr0.090.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
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_it2.4382.585950
X-RAY DIFFRACTIONr_mcbond_other2.4312.582949
X-RAY DIFFRACTIONr_mcangle_it3.4233.8531186
X-RAY DIFFRACTIONr_mcangle_other3.4243.8571187
X-RAY DIFFRACTIONr_scbond_it3.9863.1861010
X-RAY DIFFRACTIONr_scbond_other3.9773.1781008
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0924.5531461
X-RAY DIFFRACTIONr_long_range_B_refined7.39931.9142292
X-RAY DIFFRACTIONr_long_range_B_other7.38431.5882253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 48 -
Rwork0.247 946 -
obs--49.38 %

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