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- PDB-4lnx: Crystal structure of TR-alpha bound to T4 in a second site -

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Basic information

Entry
Database: PDB / ID: 4lnx
TitleCrystal structure of TR-alpha bound to T4 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 / 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 / transcription by RNA polymerase II / cell differentiation / learning or memory / 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
3,5,3'TRIIODOTHYRONINE / 3,5,3',5'-TETRAIODO-L-THYRONINE / Thyroid hormone receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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

Downloads & links

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Assembly

Deposited unit
A: Thyroid hormone receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2063
Polymers30,7781
Non-polymers1,4282
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.744, 80.924, 101.871
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
Fragment: UNP P10827 residues 148-370, UNP Q6LDR0 residues 36-75
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-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE / Levothyroxine


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.99 Å3/Da / Density % sol: 69.18 %
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: Mar 19, 2004
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→63.365 Å / Num. all: 31323 / Num. obs: 31309 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 14.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 31.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.05-2.1614.90.37520.375197.6
2.16-2.29150.2612.90.261198.1
2.29-2.45150.1834.20.183198.5
2.45-2.6514.90.12560.125198.9
2.65-2.914.90.0957.80.095199.2
2.9-3.2414.80.06910.40.069199.5
3.24-3.7414.60.05130.05199.8
3.74-4.5814.20.04214.70.042199.9
4.58-6.4813.40.03915.60.0391100
6.48-101.87112.20.036150.036199.8

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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: 2.05→37.6 Å / Occupancy max: 1.5 / Occupancy min: 0 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1573 5.03 %
Rwork0.155 --
obs0.157 31249 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 47 267 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012309
X-RAY DIFFRACTIONf_angle_d1.3753153
X-RAY DIFFRACTIONf_dihedral_angle_d16.2936
X-RAY DIFFRACTIONf_chiral_restr0.085346
X-RAY DIFFRACTIONf_plane_restr0.005403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.24681420.17982584X-RAY DIFFRACTION97
2.1162-2.19180.17351440.15582647X-RAY DIFFRACTION98
2.1918-2.27950.1691270.15542642X-RAY DIFFRACTION98
2.2795-2.38330.1951310.14982668X-RAY DIFFRACTION98
2.3833-2.50890.19841400.15052654X-RAY DIFFRACTION98
2.5089-2.6660.19131280.15842672X-RAY DIFFRACTION99
2.666-2.87180.18771380.16352718X-RAY DIFFRACTION99
2.8718-3.16070.18651550.16462700X-RAY DIFFRACTION99
3.1607-3.61770.19831570.14882723X-RAY DIFFRACTION99
3.6177-4.55670.13981670.13322760X-RAY DIFFRACTION100
4.5567-37.6040.17181440.17122908X-RAY DIFFRACTION100
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)
18.67047.26-7.72427.1359-6.79777.3714-0.73640.3431-0.2418-0.04130.19680.35281.2738-0.66510.36340.410.00690.15410.3171-0.05750.366614.43413.72350.9385
22.19923.6846-1.58698.7911-4.65863.56140.1026-0.45360.09310.3765-0.2313-0.1307-0.07340.04170.10070.1477-0.00540.040.3143-0.01020.102424.085221.871351.0124
31.6355-0.0539-0.22182.7507-1.75442.63020.13410.09710.2850.07220.31530.5167-0.4098-0.532-0.37840.20450.03750.02330.23480.0420.274124.952942.648431.4139
47.6561-0.54364.02991.7117-1.09784.6842-0.27620.04590.39430.0518-0.0284-0.0913-0.29920.10470.27450.13-0.0068-0.01040.1317-0.00490.091634.93629.666241.3245
52.07240.29880.40854.8598-1.28540.9851-0.00190.40940.2766-0.14280.21150.6171-0.1414-0.4458-0.16530.16890.0239-0.04020.3230.08120.247418.540434.992726.6021
63.24281.19820.50572.4701-0.09442.5109-0.02360.1131-0.25560.04590.0042-0.05940.0914-0.00080.02750.14670.02420.02750.1384-0.01650.070728.78218.348540.8046
76.31828.7143-4.71488.957-5.43872.3881-0.25960.1284-0.3786-0.2451-0.0198-0.59660.1501-0.05230.13340.18920.02140.0170.22550.00720.271431.201928.068726.9293
87.26940.70441.13994.4019-5.36277.96620.13070.1192-0.21560.2474-0.6796-1.3166-0.31590.85240.55180.2427-0.0404-0.030.26790.06670.256439.273143.912432.1266
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 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 309 )
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 362 )
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 391 )
8X-RAY DIFFRACTION8chain 'A' and (resid 393 through 407 )

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