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- PDB-1g5y: THE 2.0 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE RXRALPHA LIG... -

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Basic information

Entry
Database: PDB / ID: 1g5y
TitleTHE 2.0 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE RXRALPHA LIGAND BINDING DOMAIN TETRAMER IN THE PRESENCE OF A NON-ACTIVATING RETINOIC ACID ISOMER.
ComponentsRETINOIC ACID RECEPTOR RXR-ALPHA
KeywordsTRANSCRIPTION / RXRalpha ligand binding domain / inactive tetramer with 2 monomers bound with an inactivating isomer of retinoic acid
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / ion binding ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. ...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 / 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
RETINOIC ACID / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 9, 2016Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Apr 25, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2726
Polymers106,6714
Non-polymers6012
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-59 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.052, 99.701, 96.281
Angle α, β, γ (deg.)90.00, 96.70, 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: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.06 %
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
*PLUS
Density % sol: 39 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMHEPES1reservoir
21.5 M1reservoirLi2SO4
310 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 17-ID20.979338
ROTATING ANODERIGAKU RU20031.54
Detector
TypeIDDetectorDate
MARRESEARCH1CCDAug 1, 1998
RIGAKU RAXIS IIC2IMAGE PLATEAug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9793381
31.541
ReflectionResolution: 2→20 Å / Num. all: 64577 / Num. obs: 64239 / % possible obs: 99.5 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.5

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Processing

Software
NameVersionClassification
MAR345data collection
HKL-2000data reduction
CNSrefinement
CNX2000refinement
HKL-2000data scaling
CNSphasing
RefinementResolution: 2→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1919145.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 6481 10.1 %RANDOM
Rwork0.2314 ---
obs-64239 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.24 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 46.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å28.65 Å2
2---5.22 Å20 Å2
3---4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 44 496 7438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 1038 9.9 %
Rwork0.32 9484 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BSXPI3.XPLCMPD1.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMCMPD2.TOP
X-RAY DIFFRACTION4CMPD1.PAR
X-RAY DIFFRACTION5CMPD2.PAR
Software
*PLUS
Name: CNX / Version: 2000 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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