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Yorodumi- PDB-6mg1: C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Ol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mg1 | |||||||||
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Title | C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2 Crystal Form | |||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / bZIP Transciption Factor DNA Methylation CpA methylation PROTEIN-DNA COMPLEX / TRANSCRIPTION / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | Function and homology information C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / histone acetyltransferase binding / positive regulation of interleukin-4 production / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / Transcriptional Regulation by VENTX / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / negative regulation of T cell proliferation / ovarian follicle development / response to endoplasmic reticulum stress / acute-phase response / liver regeneration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / neuron differentiation / chromatin DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Horton, J.R. / Cheng, X. / Yang, J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural basis for effects of CpA modifications on C/EBP beta binding of DNA. Authors: Yang, J. / Horton, J.R. / Wang, D. / Ren, R. / Li, J. / Sun, D. / Huang, Y. / Zhang, X. / Blumenthal, R.M. / Cheng, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mg1.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mg1.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mg1 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mg1 | HTTPS FTP |
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-Related structure data
Related structure data | 6mg2C 6mg3C 2e42S S: Starting model for refinement C: citing same article (ref.) |
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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: 9325.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5, PP9092 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676 #2: DNA chain | Mass: 4924.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: 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: 3.17 Å3/Da / Density % sol: 61.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.542 Å / Num. obs: 35611 / % possible obs: 80.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.63→1.69 Å / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 842 / CC1/2: 0.787 / Rpim(I) all: 0.374 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+42 / Resolution: 1.75→34.542 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→34.542 Å
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Refine LS restraints |
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LS refinement shell |
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