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- PDB-5yso: Crystal structure of Estrogen Related Receptor-3 (ERR-gamma) liga... -

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Basic information

Entry
Database: PDB / ID: 5yso
TitleCrystal structure of Estrogen Related Receptor-3 (ERR-gamma) ligand binding domain with DN200434
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / Sodium iodide symporter (NIS) / Anaplastic thyroid cancer / Estrogen-related receptor gamma / Radioiodine therapy
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor 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 / intracellular steroid hormone receptor 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 / chromatin / regulation of DNA-templated transcription / 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 / Retinoid X Receptor / Retinoid X 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. ...Oestrogen-related receptor / Retinoic acid receptor / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-90C / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsCho, S.J. / Chin, J.W. / Yoon, H.S. / Jeon, Y.H. / Bae, J.H. / Song, J.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
the korea health industry development instituteHI16C1501 Korea, Republic Of
CitationJournal: Clin.Cancer Res. / Year: 2019
Title: A Novel Orally Active Inverse Agonist of Estrogen-related Receptor Gamma (ERR gamma ), DN200434, A Booster of NIS in Anaplastic Thyroid Cancer.
Authors: Singh, T.D. / Song, J. / Kim, J. / Chin, J. / Ji, H.D. / Lee, J.E. / Lee, S.B. / Yoon, H. / Yu, J.H. / Kim, S.K. / Yoon, G.S. / Hwang, H. / Lee, H.W. / Oh, J.M. / Lee, S.W. / Lee, J. / Choi, ...Authors: Singh, T.D. / Song, J. / Kim, J. / Chin, J. / Ji, H.D. / Lee, J.E. / Lee, S.B. / Yoon, H. / Yu, J.H. / Kim, S.K. / Yoon, G.S. / Hwang, H. / Lee, H.W. / Oh, J.M. / Lee, S.W. / Lee, J. / Choi, H.S. / Na, S.Y. / Choi, W.I. / Park, Y.J. / Song, Y.S. / Kim, Y.A. / Lee, I.K. / Cho, S.J. / Jeon, Y.H.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / 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
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 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
C: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3956
Polymers81,0253
Non-polymers1,3703
Water4,053225
1
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4652
Polymers27,0081
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4652
Polymers27,0081
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4652
Polymers27,0081
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.886, 79.828, 106.714
Angle α, β, γ (deg.)90.00, 107.81, 90.00
Int Tables number5
Space group name H-MC121

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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: 27008.498 Da / Num. of mol.: 3
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-90C / 4-[5-oxidanyl-2-phenyl-1-[4-(4-propan-2-ylpiperazin-1-yl)phenyl]pent-1-enyl]phenol


Mass: 456.619 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H36N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium fluoride, 20%(w/v) PEG 3350, 10mM Barium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.501→50 Å / Num. obs: 28403 / % possible obs: 96.49 % / Redundancy: 6.8 % / CC1/2: 0.975 / Rpim(I) all: 0.043 / Net I/σ(I): 2.6
Reflection shellResolution: 2.501→2.591 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 8.2 / Rpim(I) all: 0.141 / % possible all: 76.67

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data processing
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9Q

1s9q


Resolution: 2.501→43.711 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2434 1411 4.97 %
Rwork0.1968 --
obs0.1992 28400 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→43.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 102 225 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085226
X-RAY DIFFRACTIONf_angle_d0.9387091
X-RAY DIFFRACTIONf_dihedral_angle_d6.0593180
X-RAY DIFFRACTIONf_chiral_restr0.046822
X-RAY DIFFRACTIONf_plane_restr0.005896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.59070.3271100.24592135X-RAY DIFFRACTION77
2.5907-2.69440.30121320.22992539X-RAY DIFFRACTION92
2.6944-2.81710.32551410.23292733X-RAY DIFFRACTION98
2.8171-2.96550.27461510.22662784X-RAY DIFFRACTION100
2.9655-3.15130.29841440.23092806X-RAY DIFFRACTION100
3.1513-3.39450.29041270.21732772X-RAY DIFFRACTION100
3.3945-3.7360.2431440.19612804X-RAY DIFFRACTION100
3.736-4.27620.20561340.17632799X-RAY DIFFRACTION100
4.2762-5.3860.22511630.16812784X-RAY DIFFRACTION100
5.386-43.71770.17861650.16632833X-RAY DIFFRACTION99

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