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- PDB-1xb7: X-ray structure of ERRalpha LBD in complex with a PGC-1alpha pept... -

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Basic information

Entry
Database: PDB / ID: 1xb7
TitleX-ray structure of ERRalpha LBD in complex with a PGC-1alpha peptide at 2.5A resolution
Components
  • Peroxisome proliferator activated receptor gamma coactivator 1 alpha
  • Steroid hormone receptor ERR1
KeywordsTRANSCRIPTION / nuclear hormone receptor / ligand binding domain / three-layered alpha-helical sandwich / coactivator peptide / amphipathic alpha-helix
Function / homology
Function and homology information


positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / nuclear steroid receptor activity / temperature homeostasis / intercellular bridge / intracellular glucose homeostasis ...positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / nuclear steroid receptor activity / temperature homeostasis / intercellular bridge / intracellular glucose homeostasis / response to starvation / fatty acid oxidation / response to dietary excess / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / brown fat cell differentiation / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of gluconeogenesis / digestion / steroid binding / respiratory electron transport chain / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / mRNA processing / PML body / fibrillar center / 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 / DNA-binding transcription factor binding / neuron apoptotic process / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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 / 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. / RNA recognition motif domain ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
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 / Resolution: 2.5 Å
AuthorsKallen, J. / Schlaeppi, J.M. / Bitsch, F. / Filipuzzi, I. / Schilb, A. / Riou, V. / Graham, A. / Strauss, A. / Geiser, M. / Fournier, B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Evidence for Ligand-independent Transcriptional Activation of the Human Estrogen-related Receptor {alpha} (ERR{alpha}): CRYSTAL STRUCTURE OF ERR{alpha} LIGAND BINDING DOMAIN IN COMPLEX WITH ...Title: Evidence for Ligand-independent Transcriptional Activation of the Human Estrogen-related Receptor {alpha} (ERR{alpha}): CRYSTAL STRUCTURE OF ERR{alpha} LIGAND BINDING DOMAIN IN COMPLEX WITH PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR COACTIVATOR-1{alpha}
Authors: Kallen, J. / Schlaeppi, J.M. / Bitsch, F. / Filipuzzi, I. / Schilb, A. / Riou, V. / Graham, A. / Strauss, A. / Geiser, M. / Fournier, B.
History
DepositionAug 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5543
Polymers28,4272
Non-polymers1271
Water1,51384
1
A: Steroid hormone receptor ERR1
P: Peroxisome proliferator activated receptor gamma coactivator 1 alpha
hetero molecules

A: Steroid hormone receptor ERR1
P: Peroxisome proliferator activated receptor gamma coactivator 1 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1076
Polymers56,8544
Non-polymers2542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)109.999, 109.999, 104.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11P-101-

IOD

21A-4-

HOH

31A-23-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit.

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Components

#1: Protein Steroid hormone receptor ERR1 / Estrogen-related receptor / alpha / ERR-alpha / NR3B1 / Estrogen receptor-like 1


Mass: 27033.162 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 1393.628 Da / Num. of mol.: 1 / Fragment: coactivator peptide (L3-site) / Mutation: C207A / Source method: obtained synthetically
Details: mutated PGC-1alpha coactivator peptide (L3-site) ordered from NeoSystem, France
References: UniProt: Q9UBK2
#3: Chemical ChemComp-IOD / IODIDE ION


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaCl, KI, PEG4000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 12704 / Num. obs: 12704 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 50.9 Å2 / Rsym value: 0.099 / Net I/σ(I): 27.5
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 1186 / Rsym value: 0.41 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KV6

1kv6


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.042 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 625 4.9 %RANDOM
Rwork0.21491 ---
all0.2165 12060 --
obs0.2165 12060 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å20 Å2
2---0.59 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 1 84 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211763
X-RAY DIFFRACTIONr_bond_other_d0.0020.021731
X-RAY DIFFRACTIONr_angle_refined_deg1.4472.0022384
X-RAY DIFFRACTIONr_angle_other_deg0.95333995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3555220
X-RAY DIFFRACTIONr_chiral_restr0.0760.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02336
X-RAY DIFFRACTIONr_nbd_refined0.2140.2384
X-RAY DIFFRACTIONr_nbd_other0.2220.21842
X-RAY DIFFRACTIONr_nbtor_other0.0810.21043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.25
X-RAY DIFFRACTIONr_mcbond_it0.831.51110
X-RAY DIFFRACTIONr_mcangle_it1.59921766
X-RAY DIFFRACTIONr_scbond_it2.1043653
X-RAY DIFFRACTIONr_scangle_it3.7984.5618
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 39
Rwork0.251 829

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