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Yorodumi- PDB-1nq1: TR Receptor Mutations Conferring Hormone Resistance and Reduced C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nq1 | ||||||
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Title | TR Receptor Mutations Conferring Hormone Resistance and Reduced Corepressor Release Exhibit Decreased Stability in the Nterminal LBD | ||||||
Components | Thyroid hormone receptor beta-1 | ||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / ALPHA HELICAL / LIGAND BINDING DOMAIN / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huber, B.R. / Desclozeaux, M. / West, B.L. / Cunha-Lima, S.T. / Nguyen, H.T. / Baxter, J.D. / Ingraham, H.A. / Fletterick, R.J. | ||||||
Citation | Journal: Mol.Endocrinol. / Year: 2003 Title: Thyroid hormone receptor-beta mutations conferring hormone resistance and reduced corepressor release exhibit decreased stability in the N-terminal ligand-binding domain Authors: Huber, B.R. / Desclozeaux, M. / West, B.L. / Cunha-Lima, S.T. / Nguyen, H.T. / Baxter, J.D. / Ingraham, H.A. / Fletterick, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nq1.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nq1.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nq1 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nq1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29641.256 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN / Mutation: R243Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THRB OR NR1A2 OR ERBA2 OR THR1 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: P10828 |
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#2: Chemical | ChemComp-4HY / [ |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 700 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: Flat mirror, bent monochromator |
Radiation | Monochromator: bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→80 Å / Num. all: 57150 / Num. obs: 57101 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.848 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.062 / Net I/σ(I): 22.3 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 80 Å / Num. obs: 13743 / % possible obs: 93.5 % / Num. measured all: 54104 / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THYROID HORMONE RECEPTOR BETA WITH TRIAC BOUND (unpublished data) Resolution: 2.9→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.144 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 12346 / % reflection Rfree: 10 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.226 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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