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- PDB-3hzf: Structure of TR-alfa bound to selective thyromimetic GC-1 in C2 s... -

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Basic information

Entry
Database: PDB / ID: 3hzf
TitleStructure of TR-alfa bound to selective thyromimetic GC-1 in C2 space group
ComponentsThyroid hormone receptor, alpha isoform 1 variant
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / LIGAND BINDING DOMAIN / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
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 / sequence-specific DNA binding / transcription by RNA polymerase II / learning or memory / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / 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 alpha / Thyroid hormone receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAparicio, R. / Bleicher, L. / Polikarpov, I.
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. / Santos, M.A. / 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. / Santos, M.A. / 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
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_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

Downloads & links

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Assembly

Deposited unit
A: Thyroid hormone receptor, alpha isoform 1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3352
Polymers31,0061
Non-polymers3281
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.799, 78.777, 43.071
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thyroid hormone receptor, alpha isoform 1 variant


Mass: 31006.211 Da / Num. of mol.: 1 / Fragment: residues 135-397
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): B834 / References: UniProt: Q59FW3, UniProt: P10827*PLUS
#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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.2M sodium acetate, 100mM sodium cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, 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: Nov 25, 2003 / Details: OSMIC confocal Max-Flux
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→44.72 Å / Num. all: 9551 / Num. obs: 9092 / % possible obs: 91.61 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.366 / % possible all: 83.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSX

1bsx


Resolution: 2.5→44.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.576 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.078 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26293 459 4.8 %RANDOM
Rwork0.1884 ---
obs0.19188 9092 91.61 %-
all-9551 --
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: 34.105 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å2-2.55 Å2
2---2.55 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 24 19 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9912958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21097
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.51317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44822138
X-RAY DIFFRACTIONr_scbond_it2.4383871
X-RAY DIFFRACTIONr_scangle_it3.8644.5820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 31
Rwork0.214 603
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)
115.6367-0.4138-9.511210.3339-3.63536.34120.25460.7807-0.0944-0.4338-0.3527-0.5088-1.80840.06640.09810.1769-0.06360.04650.20710.0330.25046.3285-29.567121.3871
20.82240.5042-0.47372.968-0.97822.6360.00610.06480.0078-0.00450.01110.0957-0.0388-0.1295-0.01720.00940.03250.00290.1169-0.01210.100220.86381.41269.9598
37.6218-26.405110.22-14.83133.341930.17811.6561-0.0957-1.61790.7234-2.1884-0.3902-2.718-1.42570.53220.192-0.0359-0.04840.2185-0.02850.349721.19029.14926.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 156
2X-RAY DIFFRACTION2A157 - 407
3X-RAY DIFFRACTION3A1

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