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- PDB-1q4x: Crystal Structure of Human Thyroid Hormone Receptor beta LBD in c... -

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Basic information

Entry
Database: PDB / ID: 1q4x
TitleCrystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24
ComponentsThyroid hormone receptor beta-1
KeywordsTRANSCRIPTION / conformational change in two framework helices upon ligand binding
Function / homology
Function and homology information


retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / thyroid hormone binding / retinal cone cell development / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / thyroid hormone binding / retinal cone cell development / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / retinoic acid receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / sensory perception of sound / chromatin DNA binding / Nuclear Receptor transcription pathway / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Thyroid hormone receptor / : / 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 ...Thyroid hormone receptor / : / 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-G24 / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBorngraeber, S. / Budny, M.J. / Chiellini, G. / Cunha-Lima, S.T. / Togashi, M. / Webb, P. / Baxter, J.D. / Scanlan, T.S. / Fletterick, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor.
Authors: Borngraeber, S. / Budny, M.J. / Chiellini, G. / Cunha-Lima, S.T. / Togashi, M. / Webb, P. / Baxter, J.D. / Scanlan, T.S. / Fletterick, R.J.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thyroid hormone receptor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3353
Polymers28,5821
Non-polymers7532
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.570, 56.570, 390.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Thyroid hormone receptor beta-1


Mass: 28582.080 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB OR NR1A2 OR ERBA2 OR THR1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10828
#2: Chemical ChemComp-G24 / [4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID / GC-24


Mass: 376.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: PEG 3350, sodium acetate, glucose, cymal-2, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.5 mg/lprotein1drop
20.1 Msodium acetate1reservoir
310 %PEG33501reservoir
40.15 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2002
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.8→24.47 Å / Num. all: 10076 / Num. obs: 9368 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.98 Å / % possible all: 81.5
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 113019
Reflection shell
*PLUS
% possible obs: 81.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Thyroid Hormone Receptor beta in complex with agonist GC-1; the crystal structure was solved in our lab, but not deposited at the PDB

Resolution: 2.8→24.47 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 500 -RANDOM
Rwork0.216 ---
all0.228 10075 --
obs0.228 9368 93 %-
Displacement parametersBiso mean: 60.08 Å2
Baniso -1Baniso -2Baniso -3
1-8.9 Å214.57 Å20 Å2
2--8.9 Å20 Å2
3----17.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-6 Å
Luzzati sigma a0.48 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 56 40 1988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.8-2.930.369450.2810.05591776.7
2.93-3.080.38620.2910.048114193.8
3.08-3.270.352650.2620.044117495.4
3.27-3.530.295700.2340.035117995.5
3.53-3.880.279480.2240.04116395.5
3.88-4.440.271630.1940.034120094.4
4.44-5.580.215640.1950.027124896.5
5.58-24.470.228830.2320.025134694.4
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31
LS refinement shell
*PLUS
Lowest resolution: 2.98 Å

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