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Yorodumi- PDB-2e43: Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+43 | ||||||
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Title | Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound to A High Affinity DNA fragment | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation ...granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Transcriptional Regulation by VENTX / embryonic placenta development / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / Nuclear events stimulated by ALK signaling in cancer / ovarian follicle development / negative regulation of T cell proliferation / response to endoplasmic reticulum stress / acute-phase response / liver regeneration / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / kinase binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / nuclear matrix / 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 / response to lipopolysaccharide / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tahirov, T.H. / Inoue-Bungo, T. / Sato, K. / Shiina, M. / Hamada, K. / Ogata, K. | ||||||
Citation | Journal: To be Published Title: Structural Basis for Flexible Base Recognition by C/Ebpbeta Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sato, K. / Shiina, M. / Hamada, K. / Ogata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e43.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e43.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 2e43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e43_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 2e43_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 2e43_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2e43_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/2e43 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/2e43 | HTTPS FTP |
-Related structure data
Related structure data | 1gtwC 1gu4SC 1gu5C 2e42C 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: DNA chain | Mass: 4937.228 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 4857.179 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 9323.767 Da / Num. of mol.: 2 / Fragment: residues 259-336 / Mutation: K269A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5 / Plasmid: PAR VECTOR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17676 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: magnesium chloride, Tris-Hcl, PEG4000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 25384 / % possible obs: 99.3 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GU4 Resolution: 2.1→42.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4405373.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.04 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→42.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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