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Yorodumi- PDB-1io4: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA COR... -
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-Basic information
Entry | Database: PDB / ID: 1io4 | ||||||
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Title | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / RUNX / RUNT / C/EBP / CBF / CORE BINDING FACTOR / AML1 / AML / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / granuloma formation / regulation of odontoblast differentiation / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / CHOP-C/EBP complex / C/EBP complex ...RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / granuloma formation / regulation of odontoblast differentiation / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of CD8-positive, alpha-beta T cell differentiation / Regulation of RUNX3 expression and activity / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / lymphocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ATF4 activates genes in response to endoplasmic reticulum stress / neuron fate commitment / regulation of osteoclast differentiation / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / mammary gland epithelial cell differentiation / myeloid cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / regulation of interleukin-6 production / hair follicle morphogenesis / mammary gland epithelial cell proliferation / histone acetyltransferase binding / positive regulation of interleukin-4 production / regulation of cell differentiation / behavioral response to pain / ubiquitin-like protein ligase binding / hemopoiesis / Response of EIF2AK4 (GCN2) to amino acid deficiency / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Transcriptional Regulation by VENTX / basement membrane / neuron development / regulation of signal transduction / embryonic placenta development / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of fat cell differentiation / chondrocyte differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / Nuclear events stimulated by ALK signaling in cancer / ovarian follicle development / response to retinoic acid / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cell maturation / response to endoplasmic reticulum stress / positive regulation of interleukin-2 production / ossification / liver development / acute-phase response / skeletal system development / central nervous system development / liver regeneration / promoter-specific chromatin binding / 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 / osteoblast differentiation / Transcriptional regulation of granulopoiesis / protein polyubiquitination / positive regulation of type II interferon production / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Tahirov, T.H. / Ogata, K. | ||||||
Citation | 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. #1: Journal: To Be Published 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1io4.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1io4.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1io4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1io4_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 1io4_full_validation.pdf.gz | 478.8 KB | Display | |
Data in XML | 1io4_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1io4_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1io4 ftp://data.pdbj.org/pub/pdb/validation_reports/io/1io4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules EF
#1: DNA chain | Mass: 8018.176 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7956.156 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 3 types, 4 molecules ABCD
#3: Protein | Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: BZIP DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17676 #4: Protein | | Mass: 13715.696 Da / Num. of mol.: 1 / Fragment: RUNT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03347 #5: Protein | | Mass: 16613.648 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08024 |
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-Non-polymers , 2 types, 11 molecules
#6: Chemical | #7: 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: 4.12 Å3/Da / Density % sol: 69.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M potassium chloride, 0.01 M magnesium chloride, 0.01 M DTT, 4.5% V/V PEG 8000, 1% V/V glycerol, 1% V/V MPD, 0.05 M MES buffer pH 5.6, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: Tahirov, T.H., (2001) Acta Crystallogr., D57, 850. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2000 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: THREE WAVELENGTH FROM GOLD DERIVATIVE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 66989 / Num. obs: 21113 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.173 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 6.2 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.246 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.7 / Rsym value: 37.2 / % possible all: 90.8 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. measured all: 66989 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→19.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 461658.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.198 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.247 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 82.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.464 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.447 |