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- PDB-3imy: Structure of TR-beta bound to selective thyromimetic GC-1 -

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Basic information

Entry
Database: PDB / ID: 3imy
TitleStructure of TR-beta bound to selective thyromimetic GC-1
ComponentsThyroid hormone receptor beta
KeywordsNUCLEAR PROTEIN receptor / Alternative splicing / Deafness / Disease mutation / DNA-binding / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription / Transcription regulation / Zinc / Zinc-finger
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 mediated signaling pathway / positive regulation of thyroid hormone mediated 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 mediated signaling pathway / positive regulation of thyroid hormone mediated 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 / transcription coactivator binding / chromatin DNA 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 / 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 / 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-B72 / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBleicher, L. / Polikarpov, L. / Aparicio, R.
CitationJournal: BMC STRUCT.BIOL. / Year: 2008
Title: Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms.
Authors: Bleicher, L. / Aparicio, R. / Nunes, F.M. / Martinez, L. / Gomes Dias, S.M. / Figueira, A.C.M. / Santos, M.A.M. / Venturelli, W.H. / da Silva, R. / Donate, P.M. / Neves, F.A. / Simeoni, L.A. ...Authors: Bleicher, L. / Aparicio, R. / Nunes, F.M. / Martinez, L. / Gomes Dias, S.M. / Figueira, A.C.M. / Santos, M.A.M. / Venturelli, W.H. / da Silva, R. / Donate, P.M. / Neves, F.A. / Simeoni, L.A. / Baxter, J.D. / Webb, P. / Skaf, M.S. / Polikarpov, I.
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: Thyroid hormone receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1832
Polymers29,8541
Non-polymers3281
Water90150
1


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

A: Thyroid hormone receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3654
Polymers59,7082
Non-polymers6572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1490 Å2
ΔGint-15 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.996, 68.996, 130.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thyroid hormone receptor beta / / Nuclear receptor subfamily 1 group A member 2


Mass: 29854.139 Da / Num. of mol.: 1 / Fragment: UNP residues 202-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBA2, NR1A2, THR1, THRB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10828
#2: Chemical ChemComp-B72 / {4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid


Mass: 328.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100mM NaCac, 1.2M NaAc, 200mM Na succinate, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. all: 12297 / Num. obs: 11916 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.55-2.643.90.57799.9
2.64-2.753.90.44699.9
2.75-2.873.90.32499.8
2.87-3.023.90.231100
3.02-3.213.90.15999.8
3.21-3.463.90.09699.9
3.46-3.813.50.08771.3
3.81-4.363.80.04999.8
4.36-5.493.90.04199.8
5.49-403.70.03199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BSX

1bsx


Resolution: 2.55→35.23 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / Isotropic thermal model: ISOTROPIC / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 591 4.97 %
Rwork0.225 --
obs0.227 11887 97 %
all-12258 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.55 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 55.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.841 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 24 50 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082055
X-RAY DIFFRACTIONf_angle_d1.372783
X-RAY DIFFRACTIONf_dihedral_angle_d19.099767
X-RAY DIFFRACTIONf_chiral_restr0.067309
X-RAY DIFFRACTIONf_plane_restr0.013354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.8070.3291660.2732806X-RAY DIFFRACTION100
2.807-3.2130.3331520.262877X-RAY DIFFRACTION100
3.213-4.0470.2641190.2232578X-RAY DIFFRACTION88
4.047-35.2350.2281540.1993035X-RAY DIFFRACTION100

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