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- PDB-3e94: Crystal structure of RXRalpha ligand binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3.0E+94
TitleCrystal structure of RXRalpha ligand binding domain in complex with tributyltin and a coactivator fragment
Components
  • Nuclear receptor coactivator 2 peptide
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / protein-ligand complex / DNA-binding / Host-virus interaction / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / Activator / Phosphoprotein
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 / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / 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 / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / positive regulation of bone mineralization / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / : / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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/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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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
ACETATE ION / tributylstannanyl / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBourguet, W. / Le Maire, A.
CitationJournal: Embo Rep. / Year: 2009
Title: Activation of RXR-PPAR heterodimers by organotin environmental endocrine disruptors
Authors: le Maire, A. / Grimaldi, M. / Roecklin, D. / Dagnino, S. / Vivat-Hannah, V. / Balaguer, P. / Bourguet, W.
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1984
Polymers28,8492
Non-polymers3492
Water2,882160
1
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2 peptide
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3978
Polymers57,6994
Non-polymers6984
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)64.028, 64.028, 111.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 27269.514 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 223-462)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#2: Protein/peptide Nuclear receptor coactivator 2 peptide / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1579.866 Da / Num. of mol.: 1 / Fragment: Nuclear Receptor box 2 (UNP residues 686-698) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence can be naturally found in Homo sapiens (human).
References: UniProt: Q15596
#3: Chemical ChemComp-TBY / tributylstannanyl / tributyltin


Mass: 290.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27Sn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: PEG 4000, ammonium acetate, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→55.571 Å / Num. all: 19039 / Num. obs: 18558 / % possible obs: 98 % / Redundancy: 8.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.3 / Num. measured all: 24155 / Num. unique all: 2630 / Rsym value: 0.455 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1T

2p1t


Resolution: 1.9→28.63 Å / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.844 / SU R Cruickshank DPI: 0.167 / SU Rfree: 0.148 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 955 -RANDOM
Rwork0.19 ---
all0.192 18044 --
obs0.192 17579 97.42 %-
Displacement parametersBiso max: 56.36 Å2 / Biso mean: 25.182 Å2 / Biso min: 13.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 30 160 1956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.206
X-RAY DIFFRACTIONr_bond_refined_d0.011
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.286 77 -
Rwork0.228 --
obs-1252 96.8 %

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