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- PDB-3a9e: Crystal structure of a mixed agonist-bound RAR-alpha and antagoni... -

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Basic information

Entry
Database: PDB / ID: 3a9e
TitleCrystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains
Components
  • (Retinoic acid receptor ...) x 2
  • 13-mer (LXXLL motif) from Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nucleus / Receptor / Transcription regulation / Structural Genomics / SPINE2-complexes / Structural Proteomics in Europe
Function / homology
Function and homology information


Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / Sertoli cell fate commitment / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors ...Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / Sertoli cell fate commitment / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors / trachea cartilage development / 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 / mesenchyme development / positive regulation of translational initiation by iron / chondroblast differentiation / Endogenous sterols / embryonic camera-type eye development / glandular epithelial cell development / maternal placenta development / protein kinase B binding / growth plate cartilage development / regulation of hematopoietic progenitor cell differentiation / negative regulation of granulocyte differentiation / positive regulation of T-helper 2 cell differentiation / prostate gland development / Regulation of lipid metabolism by PPARalpha / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cartilage development / Cytoprotection by HMOX1 / retinoic acid-responsive element binding / positive regulation of thyroid hormone mediated signaling pathway / positive regulation of interleukin-5 production / angiogenesis involved in coronary vascular morphogenesis / cardiac muscle cell differentiation / nuclear retinoic acid receptor binding / anatomical structure development / ion binding / camera-type eye development / retinoic acid binding / response to vitamin A / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / apoptotic cell clearance / limb development / nuclear thyroid hormone receptor binding / ureteric bud development / protein kinase A binding / regulation of myelination / cardiac muscle cell proliferation / Signaling by Retinoic Acid / ventricular cardiac muscle tissue morphogenesis / DNA binding domain binding / positive regulation of interleukin-13 production / nuclear steroid receptor activity / DNA-binding transcription repressor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heterocyclic compound binding / LBD domain binding / face development / alpha-actinin binding / germ cell development / locomotor rhythm / aryl hydrocarbon receptor binding / negative regulation of type II interferon production / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of interleukin-4 production / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / 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 / positive regulation of cell cycle / heart morphogenesis / response to retinoic acid / cellular response to retinoic acid / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / response to glucocorticoid / embryo implantation / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / mRNA regulatory element binding translation repressor activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 ...: / : / Retinoic acid receptor / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-754 / RETINOIC ACID / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSato, Y. / Duclaud, S. / Peluso-Iltis, C. / Poussin, P. / Moras, D. / Rochel, N. / Structural Proteomics in Europe (SPINE)
CitationJournal: Plos One / Year: 2010
Title: The Phantom Effect of the Rexinoid LG100754: structural and functional insights
Authors: Sato, Y. / Ramalanjaona, N. / Huet, T. / Potier, N. / Osz, J. / Antony, P. / Peluso-Iltis, C. / Poussin-Courmontagne, P. / Ennifar, E. / Mely, Y. / Dejaegere, A. / Moras, D. / Rochel, N.
History
DepositionOct 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor alpha
I: 13-mer (LXXLL motif) from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5495
Polymers58,8523
Non-polymers6972
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor alpha
I: 13-mer (LXXLL motif) from Nuclear receptor coactivator 2
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor alpha
I: 13-mer (LXXLL motif) from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,09810
Polymers117,7046
Non-polymers1,3944
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10900 Å2
ΔGint-72 kcal/mol
Surface area39920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.300, 105.300, 111.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Retinoic acid receptor ... , 2 types, 2 molecules AB

#1: Protein Retinoic acid receptor RXR-alpha / Retinoid X receptor alpha / Nuclear receptor subfamily 2 group B member 1


Mass: 26767.908 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rxra, Nr2b1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P28700
#2: Protein Retinoic acid receptor alpha / / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 30504.383 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10276

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Protein/peptide , 1 types, 1 molecules I

#3: Protein/peptide 13-mer (LXXLL motif) from Nuclear receptor coactivator 2


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596

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Non-polymers , 3 types, 117 molecules

#4: Chemical ChemComp-754 / (2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid


Mass: 396.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36O3
#5: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM potassium thiocyanate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 16968 / Num. obs: 15407 / % possible obs: 90.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 15.2
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1662 / Rsym value: 0.333 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKF

1dkf


Resolution: 2.75→19.882 Å / SU ML: 0.63 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 737 4.86 %RANDOM
Rwork0.2014 ---
obs0.2045 15179 90.37 %-
all-16797 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.729 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--1.086 Å20 Å20 Å2
2---1.086 Å20 Å2
3---2.1721 Å2
Refinement stepCycle: LAST / Resolution: 2.75→19.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 51 115 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023833
X-RAY DIFFRACTIONf_angle_d0.5425188
X-RAY DIFFRACTIONf_dihedral_angle_d12.2911473
X-RAY DIFFRACTIONf_chiral_restr0.034600
X-RAY DIFFRACTIONf_plane_restr0.002663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7501-2.96180.30151510.22763125100
2.9618-3.25870.29851700.21963118100
3.2587-3.72760.2821300.2251226172
3.7276-4.68620.2251210.1802266583
4.6862-19.88250.24331650.1877327398
Refinement TLS params.Method: refined / Origin x: 34.103 Å / Origin y: 62.162 Å / Origin z: 7.2991 Å
111213212223313233
T0.1329 Å20.0226 Å2-0.0205 Å2-0.0319 Å2-0.0129 Å2--0.104 Å2
L1.2469 °20.59 °2-0.1421 °2-1.4068 °2-0.3309 °2--1.1789 °2
S0.0839 Å °-0.1236 Å °0.0012 Å °0.0236 Å °-0.0551 Å °-0.1078 Å °-0.051 Å °-0.0769 Å °-0.0318 Å °
Refinement TLS groupSelection details: ALL

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