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- PDB-1dkf: CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAN... -

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Basic information

Entry
Database: PDB / ID: 1dkf
TitleCRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS
Components
  • PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)
  • PROTEIN (RETINOID X RECEPTOR-ALPHA)
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / HELICAL SANDWICH / HETERODIMER / PROTEIN-LIGAND COMPLEX / Structural Proteomics in Europe / SPINE / Structural Genomics / HORMONE-GROWTH FACTOR RECEPTOR complex
Function / homology
Function and homology information


Transcriptional regulation of granulopoiesis / Carnitine shuttle / Transcriptional regulation of white adipocyte differentiation / Signaling by Retinoic Acid / Sertoli cell fate commitment / positive regulation of binding / 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 / trachea cartilage development ...Transcriptional regulation of granulopoiesis / Carnitine shuttle / Transcriptional regulation of white adipocyte differentiation / Signaling by Retinoic Acid / Sertoli cell fate commitment / positive regulation of binding / 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 / trachea cartilage development / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / glandular epithelial cell development / visceral serous pericardium development / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / ventricular cardiac muscle cell differentiation / mesenchyme development / chondroblast differentiation / Endogenous sterols / embryonic camera-type eye development / positive regulation of translational initiation by iron / maternal placenta development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / growth plate cartilage development / protein kinase B binding / positive regulation of T-helper 2 cell differentiation / prostate gland development / angiogenesis involved in coronary vascular morphogenesis / negative regulation of granulocyte differentiation / Regulation of lipid metabolism by PPARalpha / retinoic acid-responsive element binding / negative regulation of cartilage development / Cytoprotection by HMOX1 / regulation of hematopoietic progenitor cell differentiation / nuclear protein quality control by the ubiquitin-proteasome system / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / retinoic acid binding / camera-type eye development / nuclear retinoic acid receptor binding / outflow tract septum morphogenesis / cardiac muscle cell differentiation / positive regulation of vitamin D receptor signaling pathway / TGFBR3 expression / response to vitamin A / nuclear vitamin D receptor binding / apoptotic cell clearance / Signaling by Retinoic Acid / nuclear thyroid hormone receptor binding / heterocyclic compound binding / ureteric bud development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / regulation of myelination / DNA-binding transcription repressor activity / DNA binding domain binding / ventricular cardiac muscle tissue morphogenesis / limb development / LBD domain binding / positive regulation of interleukin-4 production / positive regulation of lipoprotein transport / face development / nuclear steroid receptor activity / protein kinase A binding / negative regulation of type II interferon production / germ cell development / alpha-actinin binding / cellular response to estrogen stimulus / negative regulation of tumor necrosis factor production / monocyte differentiation / response to retinoic acid / cellular response to low-density lipoprotein particle stimulus / positive regulation of bone mineralization / cardiac muscle cell proliferation / retinoic acid receptor signaling pathway / heart morphogenesis / cellular response to retinoic acid / cell maturation / peptide binding / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of cell cycle / positive regulation of neuron differentiation / response to cytokine / embryo implantation / negative regulation of miRNA transcription / placenta development / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / hippocampus development / neural tube closure / liver development / female pregnancy
Similarity search - Function
: / : / Retinoic acid receptor / 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 ...: / : / Retinoic acid receptor / 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
Chem-BMS / OLEIC ACID / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBourguet, W. / Vivat, V. / Wurtz, J.M. / Chambon, P. / Gronemeyer, H. / Moras, D. / Structural Proteomics in Europe (SPINE)
CitationJournal: Mol.Cell / Year: 2000
Title: Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains.
Authors: Bourguet, W. / Vivat, V. / Wurtz, J.M. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionDec 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.6Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RETINOID X RECEPTOR-ALPHA)
B: PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3014
Polymers52,5682
Non-polymers7332
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.600, 116.600, 207.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PROTEIN (RETINOID X RECEPTOR-ALPHA) / RXR-ALPHA


Mass: 25968.055 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P28700
#2: Protein PROTEIN (RETINOIC ACID RECEPTOR-ALPHA) / RAR-ALPHA


Mass: 26600.010 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-BMS / 4-[(4,4-DIMETHYL-1,2,3,4-TETRAHYDRO-[1,2']BINAPTHALENYL-7-CARBONYL)-AMINO]-BENZOIC ACID


Mass: 450.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H26N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growpH: 7.25 / Details: PEG 10000, pH 7.25
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
2PEG1000011

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 29168 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.204 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.3 Å2
Reflection shell
*PLUS
% possible obs: 98.4 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.262 1286 RANDOM
Rwork0.203 --
obs0.203 26091 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 54 157 3743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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