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- PDB-1xdk: Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain H... -

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Basic information

Entry
Database: PDB / ID: 1xdk
TitleCrystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator
Components
  • Retinoic acid receptor RXR-alpha
  • Retinoic acid receptor, beta
  • Thyroid Receptor Associated Protein 220
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / Nuclear Receptor / Coactivator / Ligand / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


Generic Transcription Pathway / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / Carnitine metabolism / nuclear receptor binding => GO:0016922 / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors ...Generic Transcription Pathway / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / Carnitine metabolism / nuclear receptor binding => GO:0016922 / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / ventricular cardiac muscle cell differentiation / visceral serous pericardium development / embryonic eye morphogenesis / mesenchyme development / positive regulation of translational initiation by iron / Endogenous sterols / glandular epithelial cell development / maternal placenta development / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / growth plate cartilage development / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / thyroid hormone mediated signaling pathway / Regulation of lipid metabolism by PPARalpha / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cartilage development / multicellular organism development / Cytoprotection by HMOX1 / retinoic acid-responsive element binding / regulation of vitamin D receptor signaling pathway / embryonic digestive tract development / positive regulation of thyroid hormone mediated signaling pathway / Estrogen-dependent gene expression / angiogenesis involved in coronary vascular morphogenesis / cardiac muscle cell differentiation / striatum development / outflow tract septum morphogenesis / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / neural precursor cell proliferation / anatomical structure development / positive regulation of keratinocyte differentiation / ion binding / camera-type eye development / embryonic heart tube development / retinoic acid binding / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / negative regulation of chondrocyte differentiation / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / positive regulation of programmed cell death / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / lens development in camera-type eye / nuclear thyroid hormone receptor binding / ureteric bud development / embryonic hemopoiesis / mammary gland epithelial cell proliferation / regulation of myelination / cardiac muscle cell proliferation / positive regulation of intracellular estrogen receptor signaling pathway / megakaryocyte development / erythrocyte development / ventricular cardiac muscle tissue morphogenesis / DNA binding domain binding / nuclear steroid receptor activity / regulation of branching involved in prostate gland morphogenesis / cellular response to hepatocyte growth factor stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to steroid hormone stimulus / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / transcription factor binding / negative regulation of neuron differentiation / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / animal organ regeneration / positive regulation of bone mineralization / ubiquitin ligase complex / nuclear retinoid X receptor binding / heart morphogenesis / intracellular steroid hormone receptor signaling pathway / response to retinoic acid
Similarity search - Function
Retinoic acid receptor / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / 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. ...Retinoic acid receptor / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / 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
(9cis)-retinoic acid / Retinoic acid receptor beta / Retinoic acid receptor RXR-alpha / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPogenberg, V. / Guichou, J.F. / Vivat-Hannah, V. / Kammerer, S. / Perez, E. / Germain, P. / De Lera, A.R. / Gronemeyer, H. / Royer, C.A. / Bourguet, W.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: CHARACTERIZATION OF THE INTERACTION BETWEEN RAR/RXR HETERODIMERS AND TRANSCRIPTIONAL COACTIVATORS THROUGH STRUCTURAL AND FLUORESCENCE ANISOTROPY STUDIES
Authors: Pogenberg, V. / Guichou, J.F. / Vivat-Hannah, V. / Kammerer, S. / Perez, E. / Germain, P. / De Lera, A.R. / Gronemeyer, H. / Royer, C.A. / Bourguet, W.
History
DepositionSep 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2016Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 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: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor, beta
C: Thyroid Receptor Associated Protein 220
D: Thyroid Receptor Associated Protein 220
E: Retinoic acid receptor RXR-alpha
F: Retinoic acid receptor, beta
G: Thyroid Receptor Associated Protein 220
H: Thyroid Receptor Associated Protein 220
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,75712
Polymers127,5558
Non-polymers1,2024
Water21612
1
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor, beta
C: Thyroid Receptor Associated Protein 220
D: Thyroid Receptor Associated Protein 220
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3796
Polymers63,7784
Non-polymers6012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-31 kcal/mol
Surface area20520 Å2
MethodPISA
2
E: Retinoic acid receptor RXR-alpha
F: Retinoic acid receptor, beta
G: Thyroid Receptor Associated Protein 220
H: Thyroid Receptor Associated Protein 220
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3796
Polymers63,7784
Non-polymers6012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-31 kcal/mol
Surface area20490 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-79 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.7, 115.7, 247.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Retinoic acid receptor RXR-alpha


Mass: 26579.727 Da / Num. of mol.: 2 / Fragment: Ligand-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rxra, Nr2b1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28700
#2: Protein Retinoic acid receptor, beta / / RAR-beta


Mass: 33978.113 Da / Num. of mol.: 2 / Fragment: Ligand-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rarb, Nr1b2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22605
#3: Protein/peptide
Thyroid Receptor Associated Protein 220 / TRAP220


Mass: 1609.910 Da / Num. of mol.: 4 / Fragment: Nuclear Receptor Box 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse).
References: UniProt: Q8BX19, UniProt: Q925J9*PLUS
#4: Chemical
ChemComp-9CR / (9cis)-retinoic acid / Alitretinoin


Mass: 300.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.6 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 291 K / pH: 7.5
Details: PEG 3350, Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2003
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.9→36.21 Å / Num. obs: 42989 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 92 Å2 / Rsym value: 0.083 / Net I/σ(I): 5.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRUNCATED VERSION OF PDB ENTRY 1DKF

1dkf


Resolution: 2.9→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1372 3.2 %RANDOM
Rwork0.253 ---
obs0.253 42989 99.6 %-
all-43207 --
Solvent computationBsol: 53.7918 Å2 / ksol: 0.345913 e/Å3
Displacement parametersBiso mean: 73.3 Å2
Baniso -1Baniso -2Baniso -3
1-15.57 Å214.54 Å20 Å2
2--15.57 Å20 Å2
3----31.14 Å2
Refine analyzeLuzzati coordinate error free: 0.56 Å / Luzzati sigma a free: 0.8 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7582 0 88 12 7682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.87
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 220 3.1 %
Rwork0.412 6791 -
obs--99.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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