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- PDB-3gws: Crystal Structure of T3-Bound Thyroid Hormone Receptor -

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Basic information

Entry
Database: PDB / ID: 3gws
TitleCrystal Structure of T3-Bound Thyroid Hormone Receptor
ComponentsThyroid hormone receptor beta
KeywordsHormone activator / Thyroid hormone receptor / T3 / hinge / 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
3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Polikarpov, I. / Baxter, J.D. / Webb, P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function
Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / de Oliveira Neto, M. / Fischer, H. / Togashi, M. / ...Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / de Oliveira Neto, M. / Fischer, H. / Togashi, M. / Craievich, A.F. / Garratt, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionApr 28, 2009ID: 2H6W
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Thyroid hormone receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2592
Polymers29,6081
Non-polymers6511
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.974, 68.974, 131.247
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: 29607.855 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (UNP residues 202 to 460)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB, ERBA2, NR1A2, THR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10828
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100MM SODIUM CACODYLATE, 1.4M SODIUM ACETATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5478 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.2→24.667 Å / Num. all: 18952 / Num. obs: 18232 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 42.844 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2583 / Rsym value: 0.618 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H6W

2h6w
PDB Unreleased entry


Resolution: 2.2→24.667 Å / SU ML: 1.41 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1471 5.07 %RANDOM
Rwork0.1909 ---
obs0.193 29016 81.83 %-
all-35459 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.973 Å2 / ksol: 0.308 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→24.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 23 175 2132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_deg0.709
X-RAY DIFFRACTIONf_dihedral_angle_d16.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2710.33291280.29122268X-RAY DIFFRACTION74
2.271-2.35210.32041510.26952197X-RAY DIFFRACTION74
2.3521-2.44620.27631200.22722354X-RAY DIFFRACTION76
2.4462-2.55750.25311260.21142426X-RAY DIFFRACTION78
2.5575-2.69210.21341460.19832400X-RAY DIFFRACTION80
2.6921-2.86060.22461240.19752511X-RAY DIFFRACTION81
2.8606-3.08110.23251390.2042583X-RAY DIFFRACTION85
3.0811-3.39040.25641550.18752687X-RAY DIFFRACTION88
3.3904-3.87940.18211160.16732718X-RAY DIFFRACTION88
3.8794-4.88140.18631230.15032712X-RAY DIFFRACTION88
4.8814-24.66810.21631430.17532689X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0102-0.16250.00180.0124-0.1458-0.0621-0.7268-0.26180.9284-0.88680.37680.17940.65120.28360.00050.79720.0206-0.22330.44310.12070.3178-2.339836.3251-7.1945
20.6319-0.3634-0.34031.0230.72671.20380.081-0.0020.4712-0.6155-0.1939-0.599-1.09190.50750.0110.3093-0.14410.0350.23420.07730.251810.458637.473210.2116
30.2118-0.42480.4810.35280.40260.3870.38780.131-0.3112-0.1225-0.6732-1.10590.37721.4728-0.00050.36910.1259-0.02610.860.37070.77316.884214.680724.6345
42.99720.1692-0.24290.531.27261.96520.1551-0.6442-0.08730.2634-0.2545-0.5362-0.0350.4095-0.00110.1524-0.0669-0.09370.33060.01440.12456.803625.751530.6351
51.8249-0.33120.15960.61670.20572.61550.01-0.30250.04450.1351-0.0474-0.3344-0.17930.29980.00040.0759-0.0291-0.01920.19220.03170.16844.269425.198324.0369
61.54960.9566-0.57531.28110.53161.1525-0.023-0.1975-0.2956-0.0729-0.2336-0.22740.13590.3676-0.00050.09390.0209-0.01440.16310.05780.17563.68618.17319.0896
70.6547-0.1047-0.17860.0227-0.08351.0285-0.23-0.04060.5775-0.035-0.17860.6169-1.0233-0.8743-0.00720.41430.0545-0.0590.2571-0.10850.4047-8.752539.832321.0236
82.70880.1231-0.88430.9001-1.38341.51880.06570.3267-0.1854-0.7133-0.1739-0.0379-0.415-0.05990.00040.22880.013-0.03250.17450.00030.16662.212330.63865.1446
92.37390.5919-0.73292.67310.4560.62470.1691-0.4029-0.20120.4999-0.0050.15880.3224-0.0969-0.00030.1639-0.0345-0.00910.2063-0.00930.3023-5.537419.351327.8705
100.04320.04150.05020.307-0.02250.15470.5059-1.04880.0910.4776-0.31780.73070.1713-0.31190.00040.4021-0.1641-0.0390.4877-0.01730.1561-0.660126.258537.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain X and resid 202:211
2X-RAY DIFFRACTION2chain X and resid 212:232
3X-RAY DIFFRACTION3chain X and resid 233:249
4X-RAY DIFFRACTION4chain X and resid 250:294
5X-RAY DIFFRACTION5chain X and resid 295:333
6X-RAY DIFFRACTION6chain X and resid 334:379
7X-RAY DIFFRACTION7chain X and resid 380:393
8X-RAY DIFFRACTION8chain X and resid 394:420
9X-RAY DIFFRACTION9chain X and resid 421:450
10X-RAY DIFFRACTION10chain X and resid 451:460

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