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- PDB-7ucd: Transcription factor FosB/JunD bZIP domain covalently modified wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ucd | ||||||
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Title | Transcription factor FosB/JunD bZIP domain covalently modified with the cysteine-targeting alpha-haloketone compound Z2159931480 | ||||||
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![]() | DNA BINDING PROTEIN / FosB / JunD / redox switch / redox sensor / transcription factor | ||||||
Function / homology | ![]() transcription factor AP-1 complex / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP ...transcription factor AP-1 complex / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / transcription repressor complex / transcription coregulator binding / response to progesterone / female pregnancy / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, A. / Machius, M.C. / Rudenko, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Chemically targeting the redox switch in AP1 transcription factor Delta FOSB. Authors: Kumar, A. / Aglyamova, G. / Yim, Y.Y. / Bailey, A.O. / Lynch, H.M. / Powell, R.T. / Nguyen, N.D. / Rosenthal, Z. / Zhao, W.N. / Li, Y. / Chen, J. / Fan, S. / Lee, H. / Russell, W.K. / ...Authors: Kumar, A. / Aglyamova, G. / Yim, Y.Y. / Bailey, A.O. / Lynch, H.M. / Powell, R.T. / Nguyen, N.D. / Rosenthal, Z. / Zhao, W.N. / Li, Y. / Chen, J. / Fan, S. / Lee, H. / Russell, W.K. / Stephan, C. / Robison, A.J. / Haggarty, S.J. / Nestler, E.J. / Zhou, J. / Machius, M. / 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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 710 KB | Display | ![]() |
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Full document | ![]() | 711.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uccC ![]() 5vpfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8267.290 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 7989.425 Da / Num. of mol.: 1 / Fragment: unp residues 266-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-MV0 / | ||
#4: Chemical | ChemComp-CL / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % / Description: Diamond shaped, size 200-300 micrometer |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris HCl pH 7.0, 40% (v/v) Ethanol / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.446→44.923 Å / Num. obs: 3060 / % possible obs: 84.9 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.085 / Rrim(I) all: 0.233 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.446→2.779 Å / Redundancy: 7 % / Rmerge(I) obs: 2.605 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 191 / CC1/2: 0.664 / Rpim(I) all: 1.019 / Rrim(I) all: 2.804 / % possible all: 72.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VPF, poly-alanine Resolution: 3.21→35.05 Å / SU ML: 0.4022 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.932 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.21→35.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.21→35.05 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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