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- PDB-6knr: Crystal structure of Estrogen-related receptor gamma ligand-bindi... -

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Basic information

Entry
Database: PDB / ID: 6knr
TitleCrystal structure of Estrogen-related receptor gamma ligand-binding domain with DN200699
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / Estrogen-related receptor gamma
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis ...AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
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 / 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 ...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 / 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
Chem-DL9 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsYoon, H. / Kim, J. / Chin, J. / Song, J. / Cho, S.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: An orally available inverse agonist of estrogen-related receptor gamma showed expanded efficacy for the radioiodine therapy of poorly differentiated thyroid cancer.
Authors: Kim, J. / Hwang, H. / Yoon, H. / Lee, J.E. / Oh, J.M. / An, H. / Ji, H.D. / Lee, S. / Cha, E. / Ma, M.J. / Kim, D.S. / Lee, S.J. / Kadayat, T.M. / Song, J. / Lee, S.W. / Jeon, J.H. / Park, K. ...Authors: Kim, J. / Hwang, H. / Yoon, H. / Lee, J.E. / Oh, J.M. / An, H. / Ji, H.D. / Lee, S. / Cha, E. / Ma, M.J. / Kim, D.S. / Lee, S.J. / Kadayat, T.M. / Song, J. / Lee, S.W. / Jeon, J.H. / Park, K.G. / Lee, I.K. / Jeon, Y.H. / Chin, J. / Cho, S.J.
History
DepositionAug 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7474
Polymers54,8402
Non-polymers9072
Water5,801322
1
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8742
Polymers27,4201
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8742
Polymers27,4201
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.916, 119.916, 125.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 27419.953 Da / Num. of mol.: 2 / Fragment: ligand-binding domain
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: Chemical ChemComp-DL9 / (E)-4-(1-(4-(1-cyclopropylpiperidin-4-yl)phenyl)-5-hydroxy-2-phenylpent-1-en-1-yl)phenol


Mass: 453.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H35NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.28M K Na Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 23172 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Rsym value: 0.079 / Χ2: 1.538 / Net I/σ(I): 45.2
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.149 / Num. unique obs: 23172 / CC1/2: 0.994 / Rpim(I) all: 0.041 / Rrim(I) all: 0.154 / Rsym value: 0.149 / Χ2: 0.907 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s9q

1s9q


Resolution: 2.804→29.835 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.2256 1073 4.64 %
Rwork0.1829 --
obs0.1848 23121 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→29.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 68 322 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083663
X-RAY DIFFRACTIONf_angle_d0.9854961
X-RAY DIFFRACTIONf_dihedral_angle_d6.3682286
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.006622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.804-2.93150.25021140.20912733X-RAY DIFFRACTION100
2.9315-3.08590.22881520.20232678X-RAY DIFFRACTION100
3.0859-3.2790.2511470.19312686X-RAY DIFFRACTION100
3.279-3.53180.23841350.18452733X-RAY DIFFRACTION100
3.5318-3.88660.21031140.1642743X-RAY DIFFRACTION100
3.8866-4.44740.18781410.14842745X-RAY DIFFRACTION100
4.4474-5.59720.22011180.17462799X-RAY DIFFRACTION100
5.5972-29.8350.24081520.21342931X-RAY DIFFRACTION100

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