- PDB-4rwv: Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liv... -
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Basic information
Entry
Database: PDB / ID: 4rwv
Title
Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution
Components
(Nuclear receptor ...) x 2
Keywords
TRANSCRIPTION / Ligand-binding domain of nuclear hormone receptor / PF00104 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information
nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / : / negative regulation of steroid biosynthetic process / Regulation of gene expression in early pancreatic precursor cells / AF-2 domain binding / pancreas morphogenesis / calcineurin-mediated signaling / gonad development ...nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / : / negative regulation of steroid biosynthetic process / Regulation of gene expression in early pancreatic precursor cells / AF-2 domain binding / pancreas morphogenesis / calcineurin-mediated signaling / gonad development / pituitary gland development / acinar cell differentiation / tissue development / chromatin => GO:0000785 / negative regulation of intracellular steroid hormone receptor signaling pathway / Leydig cell differentiation / male sex determination / bile acid metabolic process / embryo development ending in birth or egg hatching / adrenal gland development / hypothalamus development / homeostatic process / transcription factor binding / centriolar satellite / response to immobilization stress / positive regulation of viral genome replication / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / transcription initiation at RNA polymerase II promoter / SUMOylation of intracellular receptors / protein localization / negative regulation of DNA-binding transcription factor activity / phospholipid binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function
Nuclear receptor repeat / Nuclear receptor repeat / Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / 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 receptor repeat / Nuclear receptor repeat / Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / 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-PIZ / Nuclear receptor DAX-1 / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 1 Similarity search - Component
Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
LRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, ...LRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, NR5A2_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQS. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A SERINE (S) FOLLOWED BY AMINO ACID RESIDUES 294-541 OF THE TARGET SEQUENCE. PEPTIDE CORRESPONDING TO THE DAX1 (NUCLEAR RECEPTOR DAX1, NR0B1, UNIPROT F1D8P4_HUMAN) RESIDUES 140-PRQGSILYSLLTSSK-154 WAS CO-CRYSTALLIZED WITH THE LRH-1 LBD
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop Details: LRH-1/PIP3, 20% PEG 4K, 0.2M NaOAc, 0.1M Tris (8.5), 0.036mM PIP3, 0.90mM 15-mer PRQGSILYSLLTSSK, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
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