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- PDB-1xzx: Thyroxine-Thyroid Hormone Receptor Interactions -

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Basic information

Entry
Database: PDB / ID: 1xzx
TitleThyroxine-Thyroid Hormone Receptor Interactions
ComponentsThyroid hormone receptor beta-1
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / HORMONE-GROWTH FACTOR 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 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
CACODYLATE ION / 3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSandler, B. / Webb, P. / Apriletti, J.W. / Huber, B.R. / Togashi, M. / Cunha Lima, S.T. / Juric, S. / Nilsson, S. / Wagner, R. / Fletterick, R.J. / Baxter, J.D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Thyroxine-thyroid hormone receptor interactions.
Authors: Sandler, B. / Webb, P. / Apriletti, J.W. / Huber, B.R. / Togashi, M. / Cunha Lima, S.T. / Juric, S. / Nilsson, S. / Wagner, R. / Fletterick, R.J. / Baxter, J.D.
History
DepositionNov 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 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
X: Thyroid hormone receptor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1868
Polymers31,7141
Non-polymers1,4737
Water1,18966
1


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

X: Thyroid hormone receptor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37316
Polymers63,4272
Non-polymers2,94614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+4/31
Buried area5100 Å2
ΔGint-77 kcal/mol
Surface area21250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.764, 68.764, 130.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11X-22-

HOH

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Components

#1: Protein Thyroid hormone receptor beta-1 /


Mass: 31713.549 Da / Num. of mol.: 1 / Fragment: ligand binding domain (residues 202-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB, ERBA2, NR1A2, THR1 / Plasmid: pet28-TRbE202 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P10828
#2: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE / Triiodothyronine


Mass: 650.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.17 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: sodium acetate, cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0972 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2001
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 16507 / Num. obs: 16507 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rsym value: 0.092 / Χ2: 0.981
Reflection shellResolution: 2.3→2.34 Å / Num. unique all: 791 / Rsym value: 0.692 / Χ2: 0.848 / % possible all: 99.1

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Processing

Software
NameClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRb-TRIAC

Resolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.546 / SU ML: 0.173 / SU R Cruickshank DPI: 0.361 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.263 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1293 10 %RANDOM
Rwork0.185 ---
all0.191 12903 --
obs0.191 12903 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 29 66 2011
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.03119830.021
X-RAY DIFFRACTIONr_bond_other_d0.00218270.02
X-RAY DIFFRACTIONr_angle_refined_deg2.3126931.965
X-RAY DIFFRACTIONr_angle_other_deg1.14542373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6032475
X-RAY DIFFRACTIONr_chiral_restr0.1513100.2
X-RAY DIFFRACTIONr_gen_planes_refined0.01521840.02
X-RAY DIFFRACTIONr_gen_planes_other0.0193990.02
X-RAY DIFFRACTIONr_nbd_refined0.2875490.2
X-RAY DIFFRACTIONr_nbd_other0.24721310.2
X-RAY DIFFRACTIONr_nbtor_other0.09811950.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.275550.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.311180.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.294330.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.29170.2
X-RAY DIFFRACTIONr_mcbond_it1.29612431.5
X-RAY DIFFRACTIONr_mcangle_it2.40819952
X-RAY DIFFRACTIONr_scbond_it3.6527403
X-RAY DIFFRACTIONr_scangle_it5.8766984.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 90
Rwork0.192 851

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