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- PDB-1nav: Thyroid Receptor Alpha in complex with an agonist selective for T... -

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Basic information

Entry
Database: PDB / ID: 1nav
TitleThyroid Receptor Alpha in complex with an agonist selective for Thyroid Receptor Beta1
Componentshormone receptor alpha 1, THRA1
KeywordsMEMBRANE PROTEIN / Nuclear receptor / Thyroid receptor / ligand / complex
Function / homology
Function and homology information


regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / female courtship behavior / regulation of lipid catabolic process / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / cartilage condensation ...regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / female courtship behavior / regulation of lipid catabolic process / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / cartilage condensation / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / thyroid gland development / general transcription initiation factor binding / retinoic acid receptor signaling pathway / TBP-class protein binding / hormone-mediated signaling pathway / response to cold / ossification / erythrocyte differentiation / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of cold-induced thermogenesis / transcription by RNA polymerase II / cell differentiation / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
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 ...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 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: hormone receptor alpha 1, THRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4413
Polymers29,9901
Non-polymers4512
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.319, 109.319, 134.652
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 hormone receptor alpha 1, THRA1


Mass: 29989.646 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 148-408)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10827
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulphate, sodium citrate, lithium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.15 Mammonium sulfate1reservoir
30.03 Msodium citrate1reservoirpH5.6
40.3 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8013 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8013 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17266 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 49.5 Å2 / Rsym value: 0.051 / Net I/σ(I): 38
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 832 / Rsym value: 0.43 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 380750 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.432

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNX2000.1refinement
HKL-2000data reduction
CNX2000.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→19.75 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 849 5 %RANDOM
Rwork0.246 ---
obs-16882 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7962 Å2 / ksol: 0.333696 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å23.62 Å20 Å2
2---2.95 Å20 Å2
3---5.91 Å2
Refine analyzeLuzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 28 28 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.551
X-RAY DIFFRACTIONc_mcangle_it2.721.2
X-RAY DIFFRACTIONc_scbond_it2.121.2
X-RAY DIFFRACTIONc_scangle_it3.331.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 130 4.7 %
Rwork0.36 2633 -
obs--100 %
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: 2.5 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_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rwork: 0.36

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