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- PDB-2pin: Thyroid receptor beta in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pin
TitleThyroid receptor beta in complex with inhibitor
ComponentsThyroid hormone receptor beta-1
KeywordsHORMONE RECEPTOR / thyroid receptor beta / nuclear receptors / inhibitors / protein-protein interactions / coregulator binding / AF-2 pocket / aromatic-beta-amino ketones / structure-based drug design / surface interacting drugs
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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 ...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-4HY / 1-(4-HEXYLPHENYL)PROP-2-EN-1-ONE / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEstebanez-Perpina, E. / Jouravel, N. / Baxter, J.D. / Guy, L.R. / Webb, P. / Fletterick, R.J.
CitationJournal: Mol.Endocrinol. / Year: 2007
Title: Structural insight into the mode of action of a direct inhibitor of coregulator binding to the thyroid hormone receptor.
Authors: Estebanez-Perpina, E. / Arnold, L.A. / Jouravel, N. / Togashi, M. / Blethrow, J. / Mar, E. / Nguyen, P. / Phillips, K.J. / Baxter, J.D. / Webb, P. / Guy, R.K. / Fletterick, R.J.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,0217
Polymers57,2482
Non-polymers1,7735
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.130, 92.870, 58.350
Angle α, β, γ (deg.)90.00, 109.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thyroid hormone receptor beta-1


Mass: 28624.186 Da / Num. of mol.: 2 / Fragment: Ligand-binding domain (residues 209-461) / Mutation: D355R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 / Gene: THRB, ERBA2, NR1A2, THR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10828
#2: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID


Mass: 621.932 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#3: Chemical ChemComp-LEG / 1-(4-HEXYLPHENYL)PROP-2-EN-1-ONE


Mass: 216.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20O
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 24968 / Num. obs: 24674
Reflection shellHighest resolution: 2.3 Å

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Processing

Software
NameClassification
ELVESrefinement
CNSrefinement
ELVESdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.256 -
Rwork0.216 -
all0.216 24968
obs-24674
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 79 320 4326

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