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Yorodumi- PDB-7qdt: Crystal structure of a mutant (P393GX) Thyroid Receptor Alpha lig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qdt | |||||||||
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Title | Crystal structure of a mutant (P393GX) Thyroid Receptor Alpha ligand binding domain designed to model dominant negative human mutations. | |||||||||
Components | Isoform Alpha-1 of Thyroid hormone receptor alpha | |||||||||
Keywords | NUCLEAR PROTEIN / Nuclear receptor / Thyroid hormone / Mutation | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Romartinez-Alonso, B. / Fairall, L. / Agostini, M. / Chatterjee, K. / Schwabe, J. | |||||||||
Funding support | European Union, 1items
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Citation | Journal: Mol.Cell.Biol. / Year: 2022 Title: Structure-Guided Approach to Relieving Transcriptional Repression in Resistance to Thyroid Hormone alpha. Authors: Romartinez-Alonso, B. / Agostini, M. / Jones, H. / McLellan, J. / Sood, D.E. / Tomkinson, N. / Marelli, F. / Gentile, I. / Visser, W.E. / Schoenmakers, E. / Fairall, L. / Privalsky, M. / ...Authors: Romartinez-Alonso, B. / Agostini, M. / Jones, H. / McLellan, J. / Sood, D.E. / Tomkinson, N. / Marelli, F. / Gentile, I. / Visser, W.E. / Schoenmakers, E. / Fairall, L. / Privalsky, M. / Moran, C. / Persani, L. / Chatterjee, K. / Schwabe, J.W.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qdt.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qdt.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/7qdt ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qdt | HTTPS FTP |
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-Related structure data
Related structure data | 2h79S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26725.896 Da / Num. of mol.: 1 / Mutation: P393GX Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THRA, EAR7, ERBA1, NR1A1, THRA1, THRA2 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: P10827 |
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#2: Chemical | ChemComp-T3 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % / Description: 200-micrometers tetragonal bipyramids |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Sodium Chloride, 0.1 M Tris pH 8.5, 1.0 M Lithium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2015 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 3→72.06 Å / Num. obs: 11208 / % possible obs: 100 % / Redundancy: 16.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.034 / Rrim(I) all: 0.139 / Net I/σ(I): 22 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1764 / CC1/2: 0.948 / Rpim(I) all: 0.17 / Rrim(I) all: 0.721 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2h79 Resolution: 3→72.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.083 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.293 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.545 Å2
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Refinement step | Cycle: LAST / Resolution: 3→72.06 Å
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Refine LS restraints |
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