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- PDB-3ilz: Structure of TR-alfa bound to selective thyromimetic GC-1 in P212... -

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Basic information

Entry
Database: PDB / ID: 3ilz
TitleStructure of TR-alfa bound to selective thyromimetic GC-1 in P212121 space group
ComponentsThyroid hormone receptor, alpha isoform 1 variant
KeywordsSIGNALING PROTEIN / nuclear receptor
Function / homology
Function and homology information


regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / female courtship behavior / negative regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of lipid catabolic process / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / regulation of thyroid hormone mediated signaling pathway / positive regulation of female receptivity / regulation of heart contraction ...regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / female courtship behavior / negative regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of lipid catabolic process / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / regulation of thyroid hormone mediated 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 / response to cold / hormone-mediated signaling pathway / 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: 1.85 Å
AuthorsAparicio, R. / Polikarpov, L. / Bleicher, L.
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
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: 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_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, alpha isoform 1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1062
Polymers30,7781
Non-polymers3281
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.914, 80.351, 102.886
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 Thyroid hormone receptor, alpha isoform 1 variant /


Mass: 30777.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1A1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.2
Details: 1.0M NaCac 0.1M NaH3OAc, pH 7.2, 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: 1.85→31.47 Å / Num. obs: 47773 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 7.8
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / Num. unique all: 2964 / Rsym value: 0.383 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSX

1bsx


Resolution: 1.85→31.47 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.763 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2172 5 %RANDOM
Rwork0.15 ---
obs0.152 45966 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 max: 95.41 Å2 / Biso mean: 29.418 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 24 477 2637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0212222
X-RAY DIFFRACTIONr_bond_other_d0.0130.022060
X-RAY DIFFRACTIONr_angle_refined_deg3.0781.9923007
X-RAY DIFFRACTIONr_angle_other_deg3.04734809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4295263
X-RAY DIFFRACTIONr_chiral_restr0.1710.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.022391
X-RAY DIFFRACTIONr_gen_planes_other0.0390.02419
X-RAY DIFFRACTIONr_nbd_refined0.2740.2624
X-RAY DIFFRACTIONr_nbd_other0.2730.22496
X-RAY DIFFRACTIONr_nbtor_other0.1350.21244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2376
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.239
X-RAY DIFFRACTIONr_mcbond_it1.7191.51330
X-RAY DIFFRACTIONr_mcangle_it2.81322177
X-RAY DIFFRACTIONr_scbond_it4.2623892
X-RAY DIFFRACTIONr_scangle_it6.1554.5830
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.306 150
Rwork0.254 2964
all-3114
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)
115.5356-2.8852-5.7731.93182.654212.7321-0.42261.0423-0.09740.30680.21870.18470.4183-0.11050.20390.1653-0.0020.03690.1716-0.00220.149311.7641.80753.259
20.86730.1832-0.321.0774-0.53510.9719-0.01540.05080.1153-0.00450.03830.0775-0.0631-0.0705-0.02290.01120.0115-0.00230.04070.00510.028427.77530.09235.244
3-4.7290.9619-0.0246-0.1656-8.73787.8570.45860.45140.78440.13620.03570.388-0.6465-0.5489-0.49440.178-0.0036-0.0070.17330.01150.177627.75838.2931.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 156
2X-RAY DIFFRACTION2A157 - 410
3X-RAY DIFFRACTION3A1

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