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Yorodumi- PDB-1ckt: CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED ... -
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-Basic information
Entry | Database: PDB / ID: 1ckt | ||||||
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Title | CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX | ||||||
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Keywords | GENE REGULATION/DNA / HIGH-MOBILITY GROUP DOMAIN / BENT DNA / PROTEIN-DRUG-DNA COMPLEX / GENE REGULATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / plasmacytoid dendritic cell activation / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair ...male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / plasmacytoid dendritic cell activation / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / positive regulation of toll-like receptor 2 signaling pathway / negative regulation of apoptotic cell clearance / positive regulation of myeloid cell differentiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / positive regulation of macrophage inflammatory protein 1 alpha production / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / C-X-C chemokine binding / bent DNA binding / positive regulation of glycogen catabolic process / glycolipid binding / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / endothelial cell chemotaxis / positive regulation of DNA ligation / eye development / positive regulation of interleukin-1 production / RAGE receptor binding / induction of positive chemotaxis / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / regulation of nucleotide-excision repair / myeloid progenitor cell differentiation / myeloid cell differentiation / macrophage activation involved in immune response / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / supercoiled DNA binding / cellular response to interleukin-7 / endothelial cell proliferation / positive regulation of monocyte chemotaxis / glycogen catabolic process / apoptotic cell clearance / myoblast proliferation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / phosphatidylserine binding / positive regulation of wound healing / protein kinase activator activity / negative regulation of DNA replication / positive regulation of activated T cell proliferation / positive regulation of sprouting angiogenesis / response to type II interferon / positive regulation of smooth muscle cell migration / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / cellular response to interleukin-1 / response to glucose / DNA polymerase binding / heterochromatin formation / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / response to glucocorticoid / transcription repressor complex / positive regulation of interferon-beta production / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of mitotic cell cycle / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / peptide binding / positive regulation of JNK cascade / lung development / base-excision repair / response to insulin / cell morphogenesis / positive regulation of neuron projection development / autophagy / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / circadian rhythm / neuron projection development / transcription corepressor activity Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å | ||||||
Authors | Ohndorf, U.-M. / Rould, M.A. / Pabo, C.O. / Lippard, S.J. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Authors: Ohndorf, U.M. / Rould, M.A. / He, Q. / Pabo, C.O. / Lippard, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckt.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckt.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ckt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckt ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4872.949 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5037.280 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 8497.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 8-78, DOMAIN A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SORAGYE-DAWLEY / Tissue: LIVER / Plasmid: PT7-HMG1BA / Species (production host): Escherichia coli / Gene (production host): HMG1 DOMAIN A (M1-F89) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63159 |
#4: Chemical | ChemComp-CPT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 69 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED HEPES, MAGNESIUM ACETATE, PEG 3350, GLYCEROL AND DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.4 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 9655 / % possible obs: 97.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 84.2 % / Rmerge(I) obs: 0.334 |
-Processing
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: TYR: TYR 77 C-TERMINAL OXYGEN OXT WAS NOT FOUND IN ELECTRON DENSITY MAP; C-TERMINAL RESIDUES 78-89 WERE NOT SEEN IN DENSITY MAP
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Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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