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- PDB-1nax: Thyroid receptor beta1 in complex with a beta-selective ligand -

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Basic information

Entry
Database: PDB / ID: 1nax
TitleThyroid receptor beta1 in complex with a beta-selective ligand
ComponentsThyroid hormone receptor beta-1
KeywordsMEMBRANE PROTEIN / Nuclear receptor / thyroid receptor / complex
Function / homology
Function and homology information


retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / 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 / thyroid hormone binding ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / 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 / thyroid hormone binding / retinoic acid receptor signaling pathway / sensory perception of sound / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / chromatin DNA binding / transcription coactivator binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / 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 ...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 / 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-IH5 / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsYe, L. / Li, Y.L. / Mellstrom, K. / Mellin, C. / Bladh, L.G. / Koehler, K. / Garg, N. / Garcia Collazo, A.M. / Litten, C. / Husman, B. ...Ye, L. / Li, Y.L. / Mellstrom, K. / Mellin, C. / Bladh, L.G. / Koehler, K. / Garg, N. / Garcia Collazo, A.M. / Litten, C. / Husman, B. / Persson, K. / Ljunggren, J. / Grover, G. / Sleph, P.G. / George, R. / Malm, J.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Thyroid receptor ligands. 1. Agonist ligands selective for the thyroid receptor beta1.
Authors: Ye, L. / Li, Y.L. / Mellstrom, K. / Mellin, C. / Bladh, L.G. / Koehler, K. / Garg, N. / Garcia Collazo, A.M. / Litten, C. / Husman, B. / Persson, K. / Ljunggren, J. / Grover, G. / Sleph, P.G. ...Authors: Ye, L. / Li, Y.L. / Mellstrom, K. / Mellin, C. / Bladh, L.G. / Koehler, K. / Garg, N. / Garcia Collazo, A.M. / Litten, C. / Husman, B. / Persson, K. / Ljunggren, J. / Grover, G. / Sleph, P.G. / George, R. / Malm, J.
History
DepositionNov 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 15, 2012Group: Other
Revision 1.4Feb 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

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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)28,8222
Polymers28,4671
Non-polymers3551
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Thyroid hormone receptor beta-1
hetero molecules

A: Thyroid hormone receptor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6444
Polymers56,9342
Non-polymers7102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3620 Å2
ΔGint-34 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 107.743, 66.896
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 beta-1


Mass: 28466.994 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 209-460)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB OR NR1A2 OR ERBA2 OR THR1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10828
#2: Chemical ChemComp-IH5 / {3,5-DICHLORO-4-[4-HYDROXY-3-(PROPAN-2-YL)PHENOXY]PHENYL}ACETIC ACID / 3,5-DICHLORO-4-[(4-HYDROXY-3-ISOPROPYLPHENOXY)PHENYL]ACETIC ACID


Mass: 355.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16Cl2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulphate, TRIS, NDSB-201, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
21.95 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.0
450 mMNDSB-2011reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 20, 2002 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.087 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 119 / Rsym value: 0.29 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. obs: 7890 / Num. measured all: 104179 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNX2000.1refinement
CCP4(SCALA)data scaling
CNX2000.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→38.26 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 390 5.1 %RANDOM
Rwork0.196 ---
all-7643 --
obs-7643 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0188 Å2 / ksol: 0.377279 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--6.98 Å20 Å2
3----8.52 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 23 33 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.251
X-RAY DIFFRACTIONc_mcangle_it2.081.2
X-RAY DIFFRACTIONc_scbond_it1.971.2
X-RAY DIFFRACTIONc_scangle_it2.931.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 62 4.9 %
Rwork0.221 1210 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3INH.PARINH.PAR
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.292 / Rfactor Rwork: 0.222

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