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- PDB-3uvv: Crystal Structure of the ligand binding domains of the thyroid re... -

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Basic information

Entry
Database: PDB / ID: 3uvv
TitleCrystal Structure of the ligand binding domains of the thyroid receptor:retinoid X receptor complexed with 3,3',5 triiodo-L-thyronine and 9-cis retinoic acid
Components
  • Retinoic acid receptor RXR-alpha
  • Thyroid hormone receptor alpha
KeywordsHORMONE RECEPTOR/HORMONE RECEPTOR / TR-RXR heterodimer / allostery / alpha helical sandwich / transactivation / HORMONE RECEPTOR-HORMONE RECEPTOR complex
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / SUMOylation of intracellular receptors / negative regulation of RNA polymerase II transcription preinitiation complex assembly / thyroid hormone binding / retinoic acid-responsive element binding / thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake ...Nuclear Receptor transcription pathway / SUMOylation of intracellular receptors / negative regulation of RNA polymerase II transcription preinitiation complex assembly / thyroid hormone binding / retinoic acid-responsive element binding / thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / 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 / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of lipid metabolic process / LBD domain binding / positive regulation of lipoprotein transport / nuclear steroid receptor activity / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / monocyte differentiation / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to low-density lipoprotein particle stimulus / response to retinoic acid / positive regulation of bone mineralization / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Recycling of bile acids and salts / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cell maturation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / TBP-class protein binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / nervous system development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / 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
(9cis)-retinoic acid / 3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsFernandez, E.J. / Putcha, B.-D.K. / Wright, E. / Brunzelle, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for negative cooperativity within agonist-bound TR:RXR heterodimers.
Authors: Putcha, B.D. / Wright, E. / Brunzelle, J.S. / Fernandez, E.J.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Nov 16, 2016Group: Non-polymer description
Revision 1.3Sep 13, 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_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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thyroid hormone receptor alpha
B: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3894
Polymers57,4382
Non-polymers9512
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.130, 165.320, 85.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thyroid hormone receptor alpha / Nuclear receptor subfamily 1 group A member 1


Mass: 30090.807 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP Residues 147-407)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: THRA, NR1A1 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04625
#2: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 27346.766 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP Residues 225-462)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P19793
#3: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE


Mass: 650.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#4: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 100 mM HEPES (pH 7.3), 200 mM Tri-Sodium citrate dihydrate, 15% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.54984 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54984 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 19341 / Num. obs: 19341 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.24 % / Biso Wilson estimate: 108.62 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.57
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.22 / % possible all: 97.5

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H77

2h77


Resolution: 2.95→27.55 Å / Cor.coef. Fo:Fc: 0.9223 / Cor.coef. Fo:Fc free: 0.8882 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 952 4.92 %RANDOM
Rwork0.2008 ---
obs0.203 19330 --
all-19341 --
Displacement parametersBiso mean: 114.37 Å2
Baniso -1Baniso -2Baniso -3
1--57.0851 Å20 Å20 Å2
2--20.6424 Å20 Å2
3---36.4427 Å2
Refine analyzeLuzzati coordinate error obs: 0.686 Å
Refinement stepCycle: LAST / Resolution: 2.95→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 45 19 3755
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013813HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.265157HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1345SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes543HARMONIC5
X-RAY DIFFRACTIONt_it3813HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4607SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3272 139 5.05 %
Rwork0.2811 2615 -
all0.2834 2754 -

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