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- PDB-3d24: Crystal structure of ligand-binding domain of estrogen-related re... -

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Basic information

Entry
Database: PDB / ID: 3d24
TitleCrystal structure of ligand-binding domain of estrogen-related receptor alpha (ERRalpha) in complex with the peroxisome proliferators-activated receptor coactivator-1alpha box3 peptide (PGC-1alpha)
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Steroid hormone receptor ERR1
KeywordsTRANSCRIPTION / nuclear receptor / ligand binding domain / coactivator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger / Polymorphism / RNA-binding / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / response to starvation / lncRNA binding / response to muscle activity / intracellular glucose homeostasis / fatty acid oxidation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / response to starvation / lncRNA binding / response to muscle activity / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / nuclear steroid receptor activity / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / intercellular bridge / digestion / steroid binding / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / RNA splicing / nuclear receptor binding / gluconeogenesis / respiratory electron transport chain / transcription coregulator activity / mitochondrion organization / transcription initiation at RNA polymerase II promoter / negative regulation of smooth muscle cell proliferation / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / fibrillar center / nuclear receptor activity / mRNA processing / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / : / positive regulation of cold-induced thermogenesis / microtubule cytoskeleton / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / DNA-binding transcription factor binding / sequence-specific DNA binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity / protein domain specific binding / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
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 / Resolution: 2.11 Å
AuthorsMoras, D. / Greschik, H. / Flaig, R. / Sato, Y. / Rochel, N. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop.
Authors: Greschik, H. / Althage, M. / Flaig, R. / Sato, Y. / Chavant, V. / Peluso-Iltis, C. / Choulier, L. / Cronet, P. / Rochel, N. / Schule, R. / Stromstedt, P.E. / Moras, D.
History
DepositionMay 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroid hormone receptor ERR1
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
C: Steroid hormone receptor ERR1
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Theoretical massNumber of molelcules
Total (without water)60,5024
Polymers60,5024
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Steroid hormone receptor ERR1
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Theoretical massNumber of molelcules
Total (without water)30,2512
Polymers30,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10.3 kcal/mol
Surface area10860 Å2
MethodPISA
3
C: Steroid hormone receptor ERR1
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Theoretical massNumber of molelcules
Total (without water)30,2512
Polymers30,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-8 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.400, 56.000, 96.200
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A HOMODIMER.

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Components

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


Mass: 27584.893 Da / Num. of mol.: 2 / Fragment: Ligand binding domain: Residues 278-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRA, ERR1, ESRL1, NR3B1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11474
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / PGC-1-alpha / Ligand effect modulator 6


Mass: 2665.975 Da / Num. of mol.: 2 / Fragment: Residues 198-219 / Source method: obtained synthetically
Details: Synthetic peptide with the sequence based on the fragment (residues 198-219) of human PGC-1-alpha, UniProt entry Q9UBK2 (PRGC1_HUMAN)
References: UniProt: Q9UBK2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 15% PEG 3350, 0.2 M Mg(NO3)2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 111465 / Num. obs: 109542 / % possible obs: 88.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.031 / Net I/σ(I): 26.2
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 3.2 % / Num. unique all: 2740 / Rsym value: 0.238 / % possible all: 76.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XB7

1xb7


Resolution: 2.11→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Bijvoet differences were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1584 -RANDOM
Rwork0.212 ---
all0.212 ---
obs0.212 31872 84.4 %-
Displacement parametersBiso mean: 42.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.945 Å20 Å2-1.797 Å2
2--2.119 Å20 Å2
3---3.826 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 0 272 3794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.005
X-RAY DIFFRACTIONr_angle_refined_deg1.054

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