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- PDB-1g1u: THE 2.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE RXRALPHA LIG... -

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Basic information

Entry
Database: PDB / ID: 1g1u
TitleTHE 2.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE RXRALPHA LIGAND BINDING DOMAIN IN TETRAMER IN THE ABSENCE OF LIGAND
ComponentsRETINOIC ACID RECEPTOR RXR-ALPHA
KeywordsTRANSCRIPTION / RXRalpha ligand binding domain / tetramer / absence of ligand
Function / homology
Function and homology information


retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway ...retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA binding domain binding / positive regulation of lipid metabolic process / LBD domain binding / positive regulation of lipoprotein transport / nuclear steroid receptor activity / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of cholesterol efflux / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / monocyte differentiation / response to retinoic acid / positive regulation of bone mineralization / cellular response to low-density lipoprotein particle stimulus / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of lipid metabolism by PPARalpha / cell maturation / peptide binding / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian expression / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / mRNA transcription by RNA polymerase II / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / nervous system development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / signaling receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / 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 receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Wisely, G.B. / Milburn, M.V. / Xu, H.E.
Citation
Journal: Genes Dev. / Year: 2000
Title: Structural basis for autorepression of retinoid X receptor by tetramer formation and the AF-2 helix.
Authors: Gampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Wisely, G.B. / Milburn, M.V. / Xu, H.E.
#1: Journal: Mol.Cell / Year: 2000
Title: Asymmetry in the PPARalpha/RXRalpha Crystal Structure Reveals the Molecular Basis of Heterodimerization among Nuclear Receptors
Authors: Gampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Miller, A.B. / Bledsoe, R.K. / Milburn, M.V. / Kliewer, S.A. / Willson, T.M. / Xu, H.E.
History
DepositionOct 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETINOIC ACID RECEPTOR RXR-ALPHA
B: RETINOIC ACID RECEPTOR RXR-ALPHA
C: RETINOIC ACID RECEPTOR RXR-ALPHA
D: RETINOIC ACID RECEPTOR RXR-ALPHA


Theoretical massNumber of molelcules
Total (without water)106,6714
Polymers106,6714
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-56 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.057, 99.305, 94.980
Angle α, β, γ (deg.)90.00, 97.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RETINOIC ACID RECEPTOR RXR-ALPHA


Mass: 26667.857 Da / Num. of mol.: 4 / Fragment: LIGAND BINDING DOMAIN (RESIDUES 225 - 462)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET14 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM HEPES pH 7.5, 1.5M LiSO4, 10mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
220 mMHEPES1reservoir
31.5 M1reservoirLiSO4
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 32492 / % possible obs: 99.8 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
MAR345data collection
HKL-2000data reduction
AMoREphasing
CNX2000refinement
HKL-2000data scaling
RefinementResolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 294297.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3201 10 %RANDOM
Rwork0.22 ---
obs0.22 32014 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 45.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å27.6 Å2
2---5.06 Å20 Å2
3---4.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 0 310 7208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 481 9.3 %
Rwork0.233 4671 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BSXPI3.XPL
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNX / Version: 2000 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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