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- PDB-6ucl: Transcription factor deltaFosB bZIP domain self-assembly, type-I ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ucl | ||||||
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Title | Transcription factor deltaFosB bZIP domain self-assembly, type-I crystal | ||||||
![]() | Protein fosB | ||||||
![]() | TRANSCRIPTION / activator protein-1 / basic leucine zipper / bZIP / deltaFosB / fos / jun / transcription factor / DNA-binding protein / coiled-coil | ||||||
Function / homology | ![]() NGF-stimulated transcription / response to morphine / response to corticosterone / behavioral response to cocaine / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / response to progesterone ...NGF-stimulated transcription / response to morphine / response to corticosterone / behavioral response to cocaine / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / response to progesterone / female pregnancy / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yin, Z. / Machius, M. / Rudenko, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Self-assembly of the bZIP transcription factor Delta FosB. Authors: Yin, Z. / Venkannagari, H. / Lynch, H. / Aglyamova, G. / Bhandari, M. / Machius, M. / Nestler, E.J. / Robison, A.J. / Rudenko, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.3 KB | Display | ![]() |
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PDB format | ![]() | 22.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 248.7 KB | Display | ![]() |
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Full document | ![]() | 248.6 KB | Display | |
Data in XML | ![]() | 1014 B | Display | |
Data in CIF | ![]() | 1.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uciC ![]() 6ucmC ![]() 5vpeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8267.290 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: alternative splice form; identical to the mouse sequence in the region cloned Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 17% (w/v) PEG 4000, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→50 Å / Num. obs: 4096 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Χ2: 0.953 / Net I/σ(I): 7.3 / Num. measured all: 21906 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VPE Resolution: 2.207→30.782 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 92.76 Å2 / Biso mean: 44.4932 Å2 / Biso min: 11.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.207→30.782 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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