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- PDB-7e2e: Crystal structure of the Estrogen-Related Receptor alpha (ERRalph... -

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Basic information

Entry
Database: PDB / ID: 7e2e
TitleCrystal structure of the Estrogen-Related Receptor alpha (ERRalpha) ligand-binding domain (LBD) in complex with an agonist DS45500853 and a PGC-1alpha peptide
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alphaPeroxisome proliferator-activated receptor gamma
  • Steroid hormone receptor ERR1
KeywordsTRANSCRIPTION / Nuclear receptor / Complex / agonist
Function / homology
Function and homology information


positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / response to muscle activity / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / response to muscle activity / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / nuclear steroid receptor activity / intercellular bridge / positive regulation of ATP biosynthetic process / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / adipose tissue development / energy homeostasis / brown fat cell differentiation / intracellular steroid hormone receptor signaling pathway / positive regulation of gluconeogenesis / digestion / respiratory electron transport chain / steroid binding / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / gluconeogenesis / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / negative regulation of smooth muscle cell proliferation / transcription coregulator activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / fibrillar center / PML body / mRNA processing / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / microtubule cytoskeleton / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / ubiquitin protein ligase binding / chromatin / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormone receptor ...PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Chem-HVO / IODIDE ION / Steroid hormone receptor ERR1 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsIto, S. / Shinozuka, T. / Kimura, T. / Izumi, M. / Wakabayashi, K.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Discovery of a Novel Class of ERR alpha Agonists.
Authors: Shinozuka, T. / Ito, S. / Kimura, T. / Izumi, M. / Wakabayashi, K.
History
DepositionFeb 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Steroid hormone receptor ERR1
P: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B: Steroid hormone receptor ERR1
Q: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2717
Polymers56,5754
Non-polymers6963
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.326, 71.326, 97.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12P
22Q

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A289 - 519
2112B289 - 519
1122P205 - 219
2122Q205 - 219

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, 0.000821, -0.000344), (0.000821, 1, -0.000389), (0.000344, -0.000389, -1)71.278648, -0.04136, 0.57061

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Components

#1: Protein Steroid hormone receptor ERR1 / Estrogen receptor-like 1 / Estrogen-related receptor alpha / ERR-alpha / Nuclear receptor subfamily ...Estrogen receptor-like 1 / Estrogen-related receptor alpha / ERR-alpha / Nuclear receptor subfamily 3 group B member 1


Mass: 26894.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRA, ERR1, ESRL1, NR3B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11474
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / Peroxisome proliferator-activated receptor gamma / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1393.628 Da / Num. of mol.: 2 / Mutation: C207A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-HVO / 1-[4-(3-tert-butyl-4-oxidanyl-phenoxy)phenyl]ethanone / 1-[4-(3-tert-Butyl-4-hydroxyphenoxy)phenyl]ethan-1-one


Mass: 284.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 18% (v/v) PEG 3350, 0.2 M NaI, 0.1 M HEPES (pH 7.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 13464 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 23.1
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 685

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XB7

1xb7


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 34.63 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 1381 10.3 %RANDOM
Rwork0.2501 ---
obs0.2558 12059 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 138.6 Å2 / Biso mean: 67.608 Å2 / Biso min: 30.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å2-0 Å20 Å2
2--2.66 Å2-0 Å2
3----5.32 Å2
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 43 7 3610
Biso mean--87.01 42.2 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193654
X-RAY DIFFRACTIONr_angle_refined_deg1.2642.0174946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23823.816152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.47615660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212658
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A819MEDIUM POSITIONAL0.010.5
1A864TIGHT THERMAL1.250.5
1A819MEDIUM THERMAL1.462
2P49MEDIUM POSITIONAL0.010.5
2P48TIGHT THERMAL1.270.5
2P49MEDIUM THERMAL22
LS refinement shellResolution: 2.7→2.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 95 -
Rwork0.284 846 -
all-941 -
obs--100 %
Refinement TLS params.

Method: refined / Origin y: 66.878 Å / 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 z (Å)
12.9275-0.4729-0.10083.851-1.98093.13170.0647-0.270.15930.3744-0.10220.423-0.17650.03470.03760.1072-0.0301-0.05030.1379-0.08990.300423.5025.72
22.91340.4768-0.08754.00681.88823.02590.04950.25730.1485-0.3562-0.0791-0.4357-0.15710.02050.02970.09490.0377-0.04660.14580.07810.2947.833-5.163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A289 - 519
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B289 - 519
4X-RAY DIFFRACTION2B601

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