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Yorodumi- PDB-1gu5: Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA frag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gu5 | ||||||
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Title | Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / C/EBP / 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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tahirov, T.H. / 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. / Sasaki, M. / Ogata, K. #1: Journal: Cell (Cambridge,Mass.) / Year: 2002 Title: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter Authors: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and Preliminary X-Ray Analysis of the C/Ebpbeta C-Terminal Region in Complex with DNA Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sasaki, M. / Fujikawa, A. / Kimura, K. / Sato, K. / Adachi, S. / Kamiyaogata, K. #3: Journal: Cell (Cambridge,Mass.) / Year: 2001 Title: Structural Analyses of DNA Recognition by the Aml1/ Runx-1 Runt Domain and its Allosteric Control by Cbfbeta Authors: Tahirov, T.H. / Inoue-Bungo, T. / Morii, H. / Fujikawa, A. / Sasaki, M. / Kimura, K. / Shiina, M. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K. #4: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of Aml1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K. #5: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gu5.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gu5.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1gu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gu5_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 1gu5_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 1gu5_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1gu5_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gu5 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gu5 | HTTPS FTP |
-Related structure data
Related structure data | 1gtwSC 1gu4C 2e42C 2e43C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: BZIP DOMAIN, RESIDUES 259-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676 #2: DNA chain | | Mass: 4904.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | | Mass: 4891.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: 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: 3.74 Å3/Da / Density % sol: 66 % |
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Crystal grow | pH: 6.5 Details: 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 ...Details: 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 12, 2001 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→30 Å / Num. obs: 25871 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.088 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24.364 |
Reflection shell | Resolution: 2.08→2.12 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.13 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GTW Resolution: 2.1→29.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 734912.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8637 Å2 / ksol: 0.335149 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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