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- PDB-1zgy: Structural and Biochemical Basis for Selective Repression of the ... -

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Basic information

Entry
Database: PDB / ID: 1zgy
TitleStructural and Biochemical Basis for Selective Repression of the Orphan Nuclear Receptor LRH-1 by SHP
Components
  • Nuclear receptor subfamily 0, group B, member 2
  • Peroxisome proliferator activated receptor gamma
KeywordsTRANSCRIPTION / protein-peptide complex
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / nuclear retinoic acid receptor binding / bile acid and bile salt transport / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / MECP2 regulates transcription factors ...Nuclear Receptor transcription pathway / nuclear retinoic acid receptor binding / bile acid and bile salt transport / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / nuclear thyroid hormone receptor binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / animal organ regeneration / BMP signaling pathway / long-chain fatty acid transport / response to glucose / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / Notch signaling pathway / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / placenta development / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / positive regulation of insulin secretion / lipid metabolic process / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / PPARA activates gene expression / regulation of blood pressure / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / circadian rhythm / cellular response to insulin stimulus / RNA polymerase II transcription regulator complex / transcription corepressor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear receptor activity / : / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Nuclear receptor subfamily 0 group B member 1/2 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / 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-BRL / Peroxisome proliferator-activated receptor gamma / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, Y. / Choi, M. / Suino, K. / Kovach, A. / Daugherty, J. / Kliewer, S.A. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner.
Authors: Li, Y. / Choi, M. / Suino, K. / Kovach, A. / Daugherty, J. / Kliewer, S.A. / Xu, H.E.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator activated receptor gamma
B: Nuclear receptor subfamily 0, group B, member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3023
Polymers32,9442
Non-polymers3571
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.602, 54.493, 66.497
Angle α, β, γ (deg.)90.00, 97.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator activated receptor gamma / PPAR-gamma


Mass: 31094.135 Da / Num. of mol.: 1 / Fragment: PPARgamma Ligand Binding Domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37231
#2: Protein/peptide Nuclear receptor subfamily 0, group B, member 2


Mass: 1850.203 Da / Num. of mol.: 1 / Fragment: SHP 2nd LXXLL motif / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P97947
#3: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE / Rosiglitazone


Mass: 357.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.8 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, tri-sodium citrate, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.99998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 33487 / Num. obs: 33433 / % possible obs: 100 % / Observed criterion σ(F): 32 / Observed criterion σ(I): 11165 / Biso Wilson estimate: 26.5 Å2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM6

1fm6


Resolution: 1.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1339168.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 54 8.1 %RANDOM
Rwork0.231 ---
all0.231 33487 --
obs0.231 33433 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.248 Å2 / ksol: 0.370294 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.66 Å20 Å20.44 Å2
2--0.18 Å20 Å2
3----12.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 25 158 2464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 423 8.2 %
Rwork0.338 4738 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3brl.parbrl.top

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