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- PDB-6a6k: Crystal structure of Estrogen-related Receptor-3 (ERR-gamma) liga... -

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Basic information

Entry
Database: PDB / ID: 6a6k
TitleCrystal structure of Estrogen-related Receptor-3 (ERR-gamma) ligand binding domain with DN201000
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-9S6 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYoon, H. / Kim, J. / Chin, J. / Cho, S.J. / Song, J.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Potent, Selective, and Orally Bioavailable Estrogen-Related Receptor-gamma Inverse Agonists To Restore the Sodium Iodide Symporter Function in Anaplastic Thyroid Cancer.
Authors: Kim, J. / Song, J. / Ji, H.D. / Yoo, E.K. / Lee, J.E. / Lee, S.B. / Oh, J.M. / Lee, S. / Hwang, J.S. / Yoon, H. / Kim, D.S. / Lee, S.J. / Jeong, M. / Lee, S. / Kim, K.H. / Choi, H.S. / Lee, ...Authors: Kim, J. / Song, J. / Ji, H.D. / Yoo, E.K. / Lee, J.E. / Lee, S.B. / Oh, J.M. / Lee, S. / Hwang, J.S. / Yoon, H. / Kim, D.S. / Lee, S.J. / Jeong, M. / Lee, S. / Kim, K.H. / Choi, H.S. / Lee, S.W. / Park, K.G. / Lee, I.K. / Kim, S.H. / Hwang, H. / Jeon, Y.H. / Chin, J. / Cho, S.J.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
Water1267
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)105.828, 78.571, 106.963
Angle α, β, γ (deg.)90.00, 109.19, 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


Mass: 27008.498 Da / Num. of mol.: 3 / Fragment: UNP residues 222-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG, ERR3, ERRG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62508
#2: Chemical ChemComp-9S6 / 3-[(~{E})-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.: 7 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M BIS-TRIS pH6.5, 16 %(w/v) PEG 10K, 3% MetOH

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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: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18054 / % possible obs: 97.6 % / Redundancy: 3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.241 / Num. unique obs: 857 / CC1/2: 0.855 / Rpim(I) all: 0.178 / Rrim(I) all: 0.301 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YSO

5yso


Resolution: 2.9→39.285 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.5 / Phase error: 29.18
RfactorNum. reflection% reflection
Rfree0.2633 882 4.89 %
Rwork0.2009 --
obs0.2039 18045 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 102 7 4823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094913
X-RAY DIFFRACTIONf_angle_d1.1816689
X-RAY DIFFRACTIONf_dihedral_angle_d15.3442942
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.006857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.08180.3621590.27172699X-RAY DIFFRACTION93
3.0818-3.31970.36961370.26032841X-RAY DIFFRACTION96
3.3197-3.65350.29981410.21662849X-RAY DIFFRACTION98
3.6535-4.18170.26511440.19332881X-RAY DIFFRACTION99
4.1817-5.26650.25821520.1792914X-RAY DIFFRACTION99
5.2665-39.28910.20041490.18112979X-RAY DIFFRACTION99

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