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- PDB-3r29: Crystal structure of RXRalpha ligand-binding domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3r29
TitleCrystal structure of RXRalpha ligand-binding domain complexed with corepressor SMRT2
Components
  • Nuclear receptor corepressor 2
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / nuclear receptor / transcription factor / ligand-binding domain
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of transporter activity / negative regulation of androgen receptor signaling pathway / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / regulation of cellular ketone metabolic process / 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 ...Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of transporter activity / negative regulation of androgen receptor signaling pathway / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / regulation of cellular ketone metabolic process / 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 / nuclear glucocorticoid receptor binding / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Notch binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / LBD domain binding / Regulation of MECP2 expression and activity / estrous cycle / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / 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 / nuclear retinoid X receptor binding / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / HDACs deacetylate histones / transcription coregulator binding / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Cytoprotection by HMOX1 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / 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 / negative regulation of DNA-templated transcription / chromatin binding / 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 / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding
Similarity search - Function
N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like domain superfamily / 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 receptor RXR-alpha / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, H. / Chen, L. / Chen, J. / Jiang, H. / Shen, X.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis for retinoic x receptor repression on the tetramer.
Authors: Zhang, H. / Chen, L. / Chen, J. / Jiang, H. / Shen, X.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Nuclear receptor corepressor 2
D: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)57,2104
Polymers57,2104
Non-polymers00
Water70339
1
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor RXR-alpha
C: Nuclear receptor corepressor 2
D: Nuclear receptor corepressor 2

A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor RXR-alpha
C: Nuclear receptor corepressor 2
D: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)114,4218
Polymers114,4218
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area16680 Å2
ΔGint-117 kcal/mol
Surface area37770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.220, 118.220, 84.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-30-

HOH

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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: 26856.039 Da / Num. of mol.: 2 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Protein/peptide Nuclear receptor corepressor 2 / SMRT / N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid ...SMRT / N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone receptor / T3 receptor-associating factor / TRAC / thyroid-receptor-associated corepressor / retinoic-acid-receptor-associated corepressor


Mass: 1749.171 Da / Num. of mol.: 2 / Fragment: UNP residues 2346-2361 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 15% PEG4000, 100 mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9753
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.9→118.225 Å / Num. all: 13739 / Num. obs: 13640 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 49.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 7.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSP

3nsp


Resolution: 2.9→44.77 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.839 / SU B: 20.616 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32626 651 4.9 %RANDOM
Rwork0.24004 ---
obs0.24425 12568 100 %-
all-12568 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 39 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9894861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7255443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33223.642151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.13715673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5441526
X-RAY DIFFRACTIONr_chiral_restr0.1170.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022626
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.21904
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.22468
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4910.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.52290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3223598
X-RAY DIFFRACTIONr_scbond_it1.70731448
X-RAY DIFFRACTIONr_scangle_it2.8134.51263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 42 -
Rwork0.261 835 -
obs--100 %

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