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- PDB-3jzb: Crystal Structure of TR-alfa bound to the selective thyromimetic TRIAC -

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Basic information

Entry
Database: PDB / ID: 3jzb
TitleCrystal Structure of TR-alfa bound to the selective thyromimetic TRIAC
ComponentsTHRA protein
KeywordsTRANSCRIPTION / triac / TR / thyroid / entropy / 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 / 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
Chem-4HY / Thyroid hormone receptor alpha / Thyroid hormone receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsNascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Gaining ligand selectivity in thyroid hormone receptors via entropy.
Authors: Martinez, L. / Nascimento, A.S. / Nunes, F.M. / Phillips, K. / Aparicio, R. / Dias, S.M. / Figueira, A.C. / Lin, J.H. / Nguyen, P. / Apriletti, J.W. / Neves, F.A. / Baxter, J.D. / Webb, P. / ...Authors: Martinez, L. / Nascimento, A.S. / Nunes, F.M. / Phillips, K. / Aparicio, R. / Dias, S.M. / Figueira, A.C. / Lin, J.H. / Nguyen, P. / Apriletti, J.W. / Neves, F.A. / Baxter, J.D. / Webb, P. / Skaf, M.S. / Polikarpov, I.
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THRA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4002
Polymers30,7781
Non-polymers6221
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.020, 80.825, 102.355
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 THRA protein / Thyroid hormone receptor / alpha


Mass: 30777.945 Da / Num. of mol.: 1 / Fragment: UNP residues 148-410, Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRA, hCG_1749555 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6FH41, UniProt: P10827*PLUS
#2: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID


Mass: 621.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.0M Sodium Cacodylate, 0.1M 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: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→59.98 Å / Num. all: 34729 / Num. obs: 33965 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.9 / Redundancy: 11.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24
Reflection shellResolution: 2→2.1 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4218 / Rsym value: 0.817 / % possible all: 84.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.4_159)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H79

2h79


Resolution: 2.007→51.177 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 1684 5.11 %random
Rwork0.1714 ---
obs0.1728 32969 97.08 %-
all-33961 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41 Å2 / ksol: 0.322 e/Å3
Refinement stepCycle: LAST / Resolution: 2.007→51.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 21 246 2378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142222
X-RAY DIFFRACTIONf_angle_d1.6623003
X-RAY DIFFRACTIONf_dihedral_angle_d19.612865
X-RAY DIFFRACTIONf_chiral_restr0.092324
X-RAY DIFFRACTIONf_plane_restr0.048391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.007-2.06650.30511310.24512400X-RAY DIFFRACTION92
2.0665-2.13320.26731450.20352494X-RAY DIFFRACTION94
2.1332-2.20940.21551370.182502X-RAY DIFFRACTION95
2.2094-2.29790.2291310.17362521X-RAY DIFFRACTION95
2.2979-2.40240.20471260.16852577X-RAY DIFFRACTION97
2.4024-2.52910.18741200.15192625X-RAY DIFFRACTION98
2.5291-2.68750.19731440.1562609X-RAY DIFFRACTION98
2.6875-2.8950.20161490.16182642X-RAY DIFFRACTION99
2.895-3.18630.21531370.17052661X-RAY DIFFRACTION99
3.1863-3.64730.17011410.15842685X-RAY DIFFRACTION100
3.6473-4.59480.15791670.1412715X-RAY DIFFRACTION100
4.5948-51.19410.18491560.17672854X-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)
13.9897-0.9527-1.30063.50552.62773.2119-0.46110.6821-0.20160.35720.2269-0.45011.15090.06560.41570.50680.0320.23980.3785-0.05530.532412.01961.519253.3492
21.4578-0.0253-0.47660.3234-0.07450.5913-0.0379-0.39560.00810.12060.1037-0.0186-0.0543-0.1413-0.02570.20030.00960.04950.28020.00460.17522.67821.282749.1105
30.37380.5761-0.07091.2185-0.7281.1525-0.04430.21860.2566-0.09040.22710.50510.0713-0.4036-0.21480.29980.03280.04130.30120.11220.427422.951944.934325.7392
40.7462-0.4754-0.45031.05580.01830.82610.0033-0.16720.19910.1258-0.0227-0.0979-0.15650.11230.02440.1819-0.0204-0.02380.18970.01380.165934.512632.070842.3721
50.56660.364-0.10691.4707-0.51880.7434-0.0470.27670.2498-0.18480.2790.5191-0.0856-0.4038-0.22780.20860.0152-0.04420.29350.09250.311119.051134.657827.456
60.38160.5562-0.38731.047-0.15751.6489-0.0313-0.0407-0.17940.0322-0.0145-0.08320.01210.05930.03450.14140.01570.01390.1214-0.00380.128730.961518.770641.8632
70.1184-0.1172-0.14251.2229-0.06090.5959-0.17770.2396-0.0802-0.24480.0341-0.2810.1008-0.19430.1430.20950.00230.02250.2161-0.00440.209426.591922.685229.3738
80.28090.2036-0.02810.5702-0.52660.5920.11090.0178-0.05170.1221-0.3924-0.3894-0.19980.49060.16950.0933-0.0438-0.0250.09050.07920.143939.957643.372529.6077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 144:156)A144 - 156
2X-RAY DIFFRACTION2(chain A and resid 157:181)A157 - 181
3X-RAY DIFFRACTION3(chain A and resid 184:219)A184 - 219
4X-RAY DIFFRACTION4(chain A and resid 220:262)A220 - 262
5X-RAY DIFFRACTION5(chain A and resid 263:309)A263 - 309
6X-RAY DIFFRACTION6(chain A and resid 310:356)A310 - 356
7X-RAY DIFFRACTION7(chain A and resid 357:387)A357 - 387
8X-RAY DIFFRACTION8(chain A and resid 388:407)A388 - 407

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