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- PDB-2h79: Crystal Structure of human TR alpha bound T3 in orthorhombic spac... -

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Basic information

Entry
Database: PDB / ID: 2h79
TitleCrystal Structure of human TR alpha bound T3 in orthorhombic space group
ComponentsTHRA protein
KeywordsHORMONE/GROWTH FACTOR / TR alpha / TR / T3 / HORMONE-GROWTH FACTOR 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 / regulation of heart contraction ...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 / regulation of heart contraction / cartilage condensation / 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 / learning or memory / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor alpha / Thyroid hormone receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsNascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. ...Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, H.F.M. / Craievich, A.F. / Garrat, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I.
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. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. ...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. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. / Garratt, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THRA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7332
Polymers31,0821
Non-polymers6511
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.981, 80.795, 102.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THRA protein


Mass: 31082.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLS21 (DE3) / References: UniProt: Q6FH41, UniProt: P10827*PLUS
#2: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.0 M sodium cacodylate and 0.1M sodium acetate threehydrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 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: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→63.25 Å / Num. all: 39069 / Num. obs: 39069 / % possible obs: 98.18 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.87→1.917 Å / % possible all: 7.11

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→63.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.942 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2081 5.1 %RANDOM
Rwork0.149 ---
all0.15 41150 --
obs0.15 39069 98.18 %-
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: 29.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.87→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 23 427 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0212287
X-RAY DIFFRACTIONr_angle_refined_deg3.8461.9983094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975266
X-RAY DIFFRACTIONr_chiral_restr0.2920.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021690
X-RAY DIFFRACTIONr_nbd_refined0.2670.21302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2860.2342
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.236
X-RAY DIFFRACTIONr_mcbond_it1.731.51355
X-RAY DIFFRACTIONr_mcangle_it2.88722225
X-RAY DIFFRACTIONr_scbond_it4.8093932
X-RAY DIFFRACTIONr_scangle_it6.9244.5869
LS refinement shellResolution: 1.87→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.271 156
Rwork0.234 2780
obs-2936
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)
112.19620.42894.26643.88053.110520.8447-0.343-0.62640.1406-0.30680.22430.3039-0.2620.13860.11880.1111-0.00040.00070.111300.111312.564439.1732-1.6062
21.1024-0.10770.37471.167-0.44080.97530.0009-0.0686-0.13760.01950.01490.09270.0807-0.0674-0.01590.0758-0.01210.0030.08730.00040.079727.37989.656215.7798
310.3081-0.52366.5062-4.40828.18123.1943-0.07250.1663-0.12860.204-0.0715-0.2957-0.31910.26230.1440.1464-0.03450.00160.05040.06330.101626.98311.83418.3282
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A143 - 1562 - 15
22A157 - 40716 - 266
33B1

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