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Yorodumi- PDB-1hjc: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN BOUND TO A ... -
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-Basic information
Entry | Database: PDB / ID: 1hjc | ||||||
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Title | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN 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 / ONCOPROTEIN / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information regulation of hair follicle cell proliferation / Organic cation transport / 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 ...regulation of hair follicle cell proliferation / Organic cation transport / 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 / 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 / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / hair follicle morphogenesis / regulation of cell differentiation / behavioral response to pain / hemopoiesis / basement membrane / neuron development / regulation of signal transduction / chondrocyte differentiation / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / ossification / liver development / skeletal system development / central nervous system development / promoter-specific chromatin binding / neuron differentiation / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / 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 / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hjc.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hjc.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hjc_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 1hjc_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1hjc_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1hjc_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hjc ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hjc | HTTPS FTP |
-Related structure data
Related structure data | 1hjbC 1io4SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | CHAIN AND DNA DUPLEX |
-Components
#1: Protein | Mass: 13715.696 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03347 #2: DNA chain | Mass: 4945.200 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #3: DNA chain | Mass: 4852.170 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #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: 3.28 Å3/Da / Density % sol: 61.3 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M AMMONIUM ACETATE, 0.15 M MAGNESIUM ACETATE, 5% W/V PEG 4000, 50 MM HEPES BUFFER, PH 7.0 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 |
Detector | Type: RIGAKU RAXIS4 / Detector: IMAGE PLATE / Date: Jun 10, 2000 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. obs: 17550 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.436 % / Biso Wilson estimate: 40.9 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 2.91 % / Mean I/σ(I) obs: 10.9 / Rsym value: 0.092 / % possible all: 88.9 |
Reflection | *PLUS Num. measured all: 61764 / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IO4 Resolution: 2.65→18.01 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1305275.52 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED, ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 50
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.9964 Å2 / ksol: 0.298698 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→18.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.036 / 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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