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- PDB-8k8c: Crystal structure of C/EBPalpha BZIP domain bound to a high affin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k8c | ||||||
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Title | Crystal structure of C/EBPalpha BZIP domain bound to a high affinity DNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / C/EBPalpha / DNA binding / bZIP / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / negative regulation of cyclin-dependent protein serine/threonine kinase activity / myeloid cell differentiation / positive regulation of macrophage activation / positive regulation of transcription by RNA polymerase III / interleukin-6-mediated signaling pathway / cellular response to lithium ion ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / negative regulation of cyclin-dependent protein serine/threonine kinase activity / myeloid cell differentiation / positive regulation of macrophage activation / positive regulation of transcription by RNA polymerase III / interleukin-6-mediated signaling pathway / cellular response to lithium ion / fat cell differentiation / lipid homeostasis / transcription by RNA polymerase I / inner ear development / transcription factor binding / macrophage differentiation / cellular response to organic cyclic compound / white fat cell differentiation / embryonic placenta development / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / cell maturation / Notch signaling pathway / viral process / cholesterol metabolic process / mitochondrion organization / liver development / generation of precursor metabolites and energy / lung development / cytokine-mediated signaling pathway / kinase binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, J.R. / Chen, S.Z. / Liu, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for specific DNA sequence recognition by the transcription factor NFIL3. Authors: Chen, S. / Lei, M. / Liu, K. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.4 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k86C ![]() 8k89C ![]() 8k8aC ![]() 8k8dC 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
#1: Protein | Mass: 7341.220 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 3974.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 3965.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.015 M Calcium chloride dihydrate,0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v 2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→64.27 Å / Num. obs: 20836 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 1 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.06→2.17 Å / Num. unique obs: 2979 / CC1/2: 0.938 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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