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- PDB-9tlx: Crystal structure of Brugia malayi DAF-12 ligand binding domain i... -

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Basic information

Entry
Database: PDB / ID: 9tlx
TitleCrystal structure of Brugia malayi DAF-12 ligand binding domain in complex with a coactivator peptide and delta4-dafachronic acid
Components
  • Nuclear receptor domain-containing protein
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsDNA BINDING PROTEIN / Nuclear Hormone Receptor / Transcriptional coregulators / Transcription factor / Ligand binding domain
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / response to muscle activity / response to starvation / adipose tissue development / fatty acid oxidation / lncRNA binding / temperature homeostasis ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / response to muscle activity / response to starvation / adipose tissue development / fatty acid oxidation / lncRNA binding / temperature homeostasis / response to stress / brown fat cell differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / digestion / positive regulation of gluconeogenesis / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / RNA splicing / gluconeogenesis / intracellular glucose homeostasis / nuclear receptor binding / negative regulation of smooth muscle cell proliferation / mitochondrion organization / respiratory electron transport chain / circadian regulation of gene expression / transcription coregulator activity / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / transcription initiation at RNA polymerase II promoter / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / PML body / regulation of circadian rhythm / nuclear receptor activity / mRNA processing / Regulation of RUNX2 expression and activity / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to oxidative stress / protein-containing complex assembly / negative regulation of neuron apoptotic process / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / transcription coactivator activity / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / zinc ion binding / nucleus / cytosol
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...PGC-1alpha, RNA recognition motif / PGC-1 / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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
Similarity search - Domain/homology
CITRIC ACID / Chem-DL4 / Uncharacterized protein / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMallet, M. / le Maire, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0022 France
CitationJournal: To Be Published
Title: Crystal structure of Brugia malayi DAF-12 ligand binding domain in complex with a coactivator peptide and delta4-dafachronic acid
Authors: Mallet, M. / le Maire, A.
History
DepositionDec 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor domain-containing protein
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
C: Nuclear receptor domain-containing protein
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31613
Polymers60,6424
Non-polymers1,6749
Water11,584643
1
A: Nuclear receptor domain-containing protein
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2047
Polymers30,3212
Non-polymers8835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area12440 Å2
MethodPISA
2
C: Nuclear receptor domain-containing protein
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1126
Polymers30,3212
Non-polymers7914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-10 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.293, 77.750, 90.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Nuclear receptor domain-containing protein / BMA-DAF-12 / NR LBD domain-containing protein


Mass: 28797.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bma-daf-12, BM_BM8452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4E9F2L4
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2

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Non-polymers , 4 types, 652 molecules

#3: Chemical ChemComp-DL4 / (14beta,17alpha,25R)-3-oxocholest-4-en-26-oic acid


Mass: 414.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H42O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.7→45.1 Å / Num. obs: 60374 / % possible obs: 99.88 % / Redundancy: 2 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 10.71
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 0.2581 / Num. unique obs: 11830 / CC1/2: 0.842 / CC star: 0.956 / Rrim(I) all: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.1 Å / SU ML: 0.1887 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2101 3048 5.05 %
Rwork0.1754 57324 -
obs0.1773 60372 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 116 643 4872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734373
X-RAY DIFFRACTIONf_angle_d1.11335910
X-RAY DIFFRACTIONf_chiral_restr0.0718667
X-RAY DIFFRACTIONf_plane_restr0.0106752
X-RAY DIFFRACTIONf_dihedral_angle_d15.37871699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.3541200.27582593X-RAY DIFFRACTION99.85
1.73-1.750.2811190.26632567X-RAY DIFFRACTION99.81
1.75-1.790.29361450.23852557X-RAY DIFFRACTION99.96
1.79-1.820.25681590.2212546X-RAY DIFFRACTION99.96
1.82-1.850.26151240.20832628X-RAY DIFFRACTION99.85
1.85-1.890.2667980.20482610X-RAY DIFFRACTION99.82
1.89-1.930.23641410.20032547X-RAY DIFFRACTION99.96
1.93-1.980.25881160.20542603X-RAY DIFFRACTION99.96
1.98-2.030.26171410.20692587X-RAY DIFFRACTION99.93
2.03-2.080.21171220.17842596X-RAY DIFFRACTION100
2.08-2.140.21161320.17422595X-RAY DIFFRACTION99.96
2.14-2.210.19131310.16862609X-RAY DIFFRACTION99.96
2.21-2.290.19871560.17162590X-RAY DIFFRACTION99.89
2.29-2.380.21881200.17342607X-RAY DIFFRACTION99.96
2.38-2.490.19671490.1772593X-RAY DIFFRACTION99.93
2.49-2.620.21071500.18112571X-RAY DIFFRACTION99.96
2.62-2.790.21441470.17622617X-RAY DIFFRACTION99.82
2.79-30.20711530.16422615X-RAY DIFFRACTION99.96
3-3.30.19221790.16622589X-RAY DIFFRACTION99.78
3.3-3.780.20681410.14592642X-RAY DIFFRACTION99.78
3.78-4.760.1571540.13862674X-RAY DIFFRACTION99.72
4.76-45.10.21031510.17782788X-RAY DIFFRACTION99.63

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