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- PDB-3jzc: Crystal Structure of TR-beta bound to the selective thyromimetic TRIAC -

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Basic information

Entry
Database: PDB / ID: 3jzc
TitleCrystal Structure of TR-beta bound to the selective thyromimetic TRIAC
ComponentsThyroid hormone receptor beta
KeywordsTRANSCRIPTION / TR / triac / entropy / Deafness / Disease mutation / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / retinoic acid receptor signaling pathway / sensory perception of sound / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / transcription coactivator binding / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
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-4HY / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNascimento, A.S. / Dias, S.G.M. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thyroid hormone receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7242
Polymers30,1021
Non-polymers6221
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.781, 68.781, 131.013
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thyroid hormone receptor beta / / Nuclear receptor subfamily 1 group A member 2


Mass: 30102.248 Da / Num. of mol.: 1 / Fragment: UNP residues 202-461, Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB, ERBA2, NR1A2, THR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P10828
#2: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID / Tiratricol


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 291 K / pH: 6.8
Details: 100mM Sodium Cacodylate, 1.4M sodium acetate, pH 6.8, 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
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: 2.5→35.22 Å / Num. obs: 12993 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 23
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.763 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWS

3gws


Resolution: 2.5→35.219 Å / SU ML: 0.3 / σ(F): 0.06 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 605 4.88 %
Rwork0.1982 --
obs0.2004 12407 95.73 %
all-12960 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.97 Å2 / ksol: 0.311 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→35.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 21 13 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082032
X-RAY DIFFRACTIONf_angle_d1.3082755
X-RAY DIFFRACTIONf_dihedral_angle_d18.244752
X-RAY DIFFRACTIONf_chiral_restr0.067306
X-RAY DIFFRACTIONf_plane_restr0.019352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75150.28321450.23382764X-RAY DIFFRACTION91
2.7515-3.14940.26631440.22762852X-RAY DIFFRACTION94
3.1494-3.96710.2521480.19143001X-RAY DIFFRACTION98
3.9671-35.22290.22791680.18043185X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.88691.42440.07551.9478-1.71011.79450.233-0.797-0.29050.1931-0.49020.30971.0459-0.4580.12860.4089-0.15580.06970.48920.03350.3093-19.9891-7.0649-36.8439
21.98762.02213.05697.3534-0.20983.8485-0.0936-0.42290.0088-1.5003-0.0194-2.48780.65240.05030.42290.76270.41880.43670.7268-0.06421.1787
35.7164-0.9263-1.59580.51970.27212.1384-0.11460.1593-1.1236-1.185-0.309-0.82150.42580.30060.53590.69080.1060.32810.3089-0.02420.4331
41.75391.11380.83921.92081.01212.72830.011-0.2648-0.0601-0.5539-0.2451-0.2310.2541-0.2690.12910.4488-0.0536-0.05590.2129-0.08340.2513
50.8363-0.4254-0.46131.59940.2483.3246-0.1065-0.037-0.072-0.1991-0.1025-0.42520.42970.50630.24460.24730.0890.06610.25170.01750.3788
6-3.8252-0.52574.8542.60841.16877.3453-0.2798-0.21850.8028-0.7952-0.07850.5521-0.2998-1.21090.46120.25640.0125-0.06110.3683-0.0810.4906
71.81610.9841.40392.79880.26562.98940.2282-0.42590.07690.3327-0.26340.36380.1066-0.57520.13090.2563-0.03430.04910.3236-0.06270.2814
83.97693.1326-1.72575.2814-4.4312-0.8628-0.76470.76150.3628-1.85110.4826-0.31160.6475-0.19980.2120.6311-0.1085-0.01840.2510.08830.2367
Refinement TLS groupSelection details: CHAIN A AND RESID 433:460)

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