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Yorodumi- PDB-1bsx: STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bsx | |||||||||
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Title | STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS | |||||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / NUCLEAR RECEPTORS / COACTIVATORS / GRIP1 / SPECIFICITY INTERACTION SITE / HORMONE-GROWTH FACTOR 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 / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | |||||||||
Authors | Wagner, R.L. / Darimont, B.D. / Apriletti, J.W. / Stallcup, M.R. / Kushner, P.J. / Baxter, J.D. / Fletterick, R.J. / Yamamoto, K.R. | |||||||||
Citation | Journal: Genes Dev. / Year: 1998 Title: Structure and specificity of nuclear receptor-coactivator interactions. Authors: Darimont, B.D. / Wagner, R.L. / Apriletti, J.W. / Stallcup, M.R. / Kushner, P.J. / Baxter, J.D. / Fletterick, R.J. / Yamamoto, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bsx.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bsx.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/1bsx ftp://data.pdbj.org/pub/pdb/validation_reports/bs/1bsx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.52697, 0.84909, -0.03674), Vector: |
-Components
#1: Protein | Mass: 29410.996 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: HIS-TAGGED (THE FOLLOWING RESIDUES WERE NOT SEEN IN THE ELECTRON DENSITY: MGSSHHHHHHSSGLVPRGSHM) Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P10828 #2: Protein/peptide | Mass: 1507.738 Da / Num. of mol.: 2 / Fragment: NR-BOX2 FROM NUCLEAR RECEPTOR INTERACTION DOMAIN / Source method: obtained synthetically #3: Chemical | |
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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: 2.91 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.9 / Details: pH 4.9 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 15, 1997 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→25 Å / Num. obs: 8490 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.6→3.66 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.261 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 35565 |
Reflection shell | *PLUS % possible obs: 96.3 % / Num. unique obs: 411 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN THYROID HORMONE RECEPTOR BETA Resolution: 3.7→100 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36 Å2 / ksol: 0.27 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.7→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.7 Å / Num. reflection all: 7851 / Num. reflection obs: 7614 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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