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- PDB-1hjb: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBE... -
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Basic information
Entry | Database: PDB / ID: 1hjb | ||||||
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Title | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / RUNX / RUNT / C/EBP / CBF / CORE BINDING FACTOR / AML1 / AML / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / 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 / positive regulation of cell maturation / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of CD4-positive, alpha-beta T cell differentiation / hepatocyte proliferation / 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 / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / myeloid progenitor cell differentiation / regulation of dendritic cell differentiation / definitive hemopoiesis / regulation of T cell anergy / regulation of interleukin-6 production / embryonic hemopoiesis / mammary gland epithelial cell proliferation / histone acetyltransferase binding / hair follicle morphogenesis / positive regulation of interleukin-4 production / behavioral response to pain / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / hemopoiesis / Transcriptional Regulation by VENTX / basement membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of signal transduction / neuron development / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / chondrocyte differentiation / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / negative regulation of T cell proliferation / response to retinoic acid / ovarian follicle development / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / ossification / liver development / skeletal system development / central nervous system development / acute-phase response / liver regeneration / promoter-specific chromatin binding / 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 / nuclear matrix / histone deacetylase 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 angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of type II interferon production / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Ogata, K. | ||||||
![]() | ![]() 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: 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-Bungo, 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 174 KB | Display | ![]() |
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PDB format | ![]() | 133.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 479.4 KB | Display | ![]() |
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Full document | ![]() | 521.9 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hjcC ![]() 1io4SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 10248.872 Da / Num. of mol.: 4 / Fragment: RESIDUES 259-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 13715.696 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: DNA chain | Mass: 8018.176 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 7956.156 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) ![]() Compound details | C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND ...C/EBP BETA IS IMPORTANT TRANSCRIPT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 64.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 5 MM MGSO4, 3% W/V PEG 4000, 1% V/V DIOXANE, 50 MM MES BUFFER, PH 5.6 AT 24 DEGREES C | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 297 K / Method: vapor diffusion, sitting drop / 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7085 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 26407 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 4.456 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.302 / % possible all: 71.9 |
Reflection | *PLUS Num. measured all: 117670 / Rmerge(I) obs: 0.006 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IO4 Resolution: 3→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 173187.84 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED, BSOL IS DETERMINED MANUALLY AND FIXED. ATOMS C, O, N, AND CA ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 20
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19 Å2 / ksol: 0.197986 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.033 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.36 |