+Open data
-Basic information
Entry | Database: PDB / ID: 3d57 | ||||||
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Title | TR Variant D355R | ||||||
Components | Thyroid hormone receptor beta | ||||||
Keywords | HORMONE / 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 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: 2.2 Å | ||||||
Authors | Jouravel, N. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d57.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d57.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d57 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d57 | HTTPS FTP |
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-Related structure data
Related structure data | 1naxS 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: 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 | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115891 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2004 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115891 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 5.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.37 Å / Num. reflection obs: 4168 |