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- PDB-3d57: TR Variant D355R -

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Basic information

Entry
Database: PDB / ID: 3d57
TitleTR Variant D355R
ComponentsThyroid hormone receptor beta
KeywordsHORMONE / TRANSCRIPTION RECEPTOR / thyroid hormone receptor / ligand binding domain / D355R mutant / homodimer / Alternative splicing / Deafness / Disease mutation / DNA-binding / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription / Transcription regulation / Zinc / 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 receptor signaling pathway / positive regulation of thyroid hormone receptor 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 receptor signaling pathway / positive regulation of thyroid hormone receptor 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 / chromatin DNA binding / transcription coactivator 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJouravel, N.
CitationJournal: Proteins / Year: 2008
Title: Molecular basis for dimer formation of TRbeta variant D355R.
Authors: Jouravel, N. / Sablin, E. / Togashi, M. / Baxter, J.D. / Webb, P. / Fletterick, R.J.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thyroid hormone receptor beta
B: Thyroid hormone receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5955
Polymers60,2562
Non-polymers1,3403
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.557, 92.963, 58.808
Angle α, β, γ (deg.)90.00, 110.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30127.777 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: D355R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 7068, ERBA2, NR1A2, THR1, THRB / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P10828
#2: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID


Mass: 621.932 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115891 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115891 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 31306 / Num. obs: 28545 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.069 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / Num. unique all: 4168 / Rsym value: 0.22 / % possible all: 90.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAX

1nax


Resolution: 2.2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 28545 RANDOM
Rwork0.21 --
all0.24 28545 -
obs0.21 25784 -
Displacement parametersBiso mean: 5.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.773 Å20 Å20.899 Å2
2--8.555 Å20 Å2
3----9.329 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 47 105 4069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008572
X-RAY DIFFRACTIONc_angle_deg1.19683
LS refinement shellResolution: 2.2→2.37 Å / Num. reflection obs: 4168

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