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- PDB-4lnw: Crystal structure of TR-alpha bound to T3 in a second site -

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Basic information

Entry
Database: PDB / ID: 4lnw
TitleCrystal structure of TR-alpha bound to T3 in a second site
ComponentsThyroid hormone receptor alpha
KeywordsTRANSCRIPTION / Mainly Alpha Orthogonal Bundle / Transcription factor
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 / cartilage condensation ...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 / cartilage condensation / regulation of heart contraction / 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 / cell differentiation / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPuhl, A.C. / Aparicio, R. / Polikarpov, I.
CitationJournal: Mol.Endocrinol. / Year: 2014
Title: Identification of a new hormone-binding site on the surface of thyroid hormone receptor.
Authors: Souza, P.C. / Puhl, A.C. / Martinez, L. / Aparicio, R. / Nascimento, A.S. / Figueira, A.C. / Nguyen, P. / Webb, P. / Skaf, M.S. / Polikarpov, I.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
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 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0803
Polymers30,7781
Non-polymers1,3022
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.781, 80.789, 102.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thyroid hormone receptor alpha / Nuclear receptor subfamily 1 group A member 1 / V-erbA-related protein 7 / EAR-7 / c-erbA-1 / c-erbA-alpha


Mass: 30777.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRA, EAR7, ERBA1, NR1A1, THRA1, THRA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10827
#2: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE


Mass: 650.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IN THIS ENTRY CORRESPONDS TO P10827-2, ISOFORM ALPHA-1

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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, hanging drop / pH: 7.2
Details: 1.0 M sodium cacodylate and 0.1 M sodium acetate threehydrate, 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: Oct 16, 2003
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→63.464 Å / Num. all: 39937 / Num. obs: 39906 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 8 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.9-280.3492.10.349199.9
2-2.1280.2063.70.206199.9
2.12-2.278.10.1335.70.1331100
2.27-2.458.30.0947.80.0941100
2.45-2.698.40.06810.60.0681100
2.69-38.30.05412.90.0541100
3-3.478.10.04214.80.0421100
3.47-4.257.90.03416.70.0341100
4.25-6.017.20.03317.10.0331100
6.01-102.5626.40.031180.031199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.1.9data scaling
AMoREphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.59 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 2005 5.03 %
Rwork0.158 --
obs0.16 39829 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 46 324 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092358
X-RAY DIFFRACTIONf_angle_d1.3213243
X-RAY DIFFRACTIONf_dihedral_angle_d14.658970
X-RAY DIFFRACTIONf_chiral_restr0.08355
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.24161550.1952649X-RAY DIFFRACTION100
1.9475-2.00020.19111400.18282653X-RAY DIFFRACTION100
2.0002-2.05910.19361480.16952661X-RAY DIFFRACTION100
2.0591-2.12550.20691420.15682665X-RAY DIFFRACTION100
2.1255-2.20150.20781380.15652662X-RAY DIFFRACTION100
2.2015-2.28960.18411400.15842697X-RAY DIFFRACTION100
2.2896-2.39380.19261450.15432688X-RAY DIFFRACTION100
2.3938-2.520.16051290.15362683X-RAY DIFFRACTION100
2.52-2.67780.18521390.15592680X-RAY DIFFRACTION100
2.6778-2.88450.17771260.15812726X-RAY DIFFRACTION100
2.8845-3.17460.18421390.16622715X-RAY DIFFRACTION100
3.1746-3.63370.17881390.15052731X-RAY DIFFRACTION100
3.6337-4.57680.1661670.13822753X-RAY DIFFRACTION100
4.5768-37.59190.19411580.17392861X-RAY DIFFRACTION99
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)
19.17917.2976-8.75655.8621-7.16849.0642-0.69170.3772-0.4829-0.1332-0.03250.05261.1305-0.80120.61370.4121-0.01420.20910.3353-0.08110.444414.38873.25152.3791
21.89712.4889-1.5556.8201-3.8783.3057-0.0161-0.3370.11760.49640.09530.2094-0.1305-0.1257-0.07630.17850.00480.04140.3115-0.0080.159624.223222.120951.0207
31.9828-1.58431.46653.0636-0.41961.8474-0.0158-0.0655-0.38820.73380.67591.2894-0.2539-1.5383-0.65590.37060.08820.13370.5050.16220.666115.672242.205134.0322
40.96620.1882-0.39581.9926-0.94461.78190.0090.09130.1574-0.05220.06640.1573-0.1208-0.1197-0.05430.12110.0157-0.00040.18430.00190.147328.097933.143233.7147
53.32931.2771-0.28823.80590.22742.6686-0.0947-0.021-0.31050.0697-0.0440.10360.2524-0.23240.12660.16820.00380.0470.1806-0.00450.121826.410514.206941.966
60.3520.9251-0.33416.3799-0.45761.2756-0.01190.0403-0.03840.0358-0.1166-0.32270.00490.17560.13380.12880.01750.0110.23760.03260.217834.04833.170428.1567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 145 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 333 )
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 362 )
6X-RAY DIFFRACTION6chain 'A' and (resid 363 through 407 )

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