+Open data
-Basic information
Entry | Database: PDB / ID: 1h88 | ||||||
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Title | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / TRANSCRIPTION REGULATION / BZIP / PROTO-ONCOGENE / MYB / C-MYB / C/EBP | ||||||
Function / homology | Function and homology information C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / embryonic digestive tract development / stem cell division / mammary gland epithelial cell differentiation / myeloid cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / cellular response to interleukin-6 / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / WD40-repeat domain binding / 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 / Transcriptional Regulation by VENTX / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of collagen biosynthetic process / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / negative regulation of T cell proliferation / ovarian follicle development / positive regulation of glial cell proliferation / spleen development / response to endoplasmic reticulum stress / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / acute-phase response / liver regeneration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / neuron differentiation / chromatin DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / G1/S transition of mitotic cell cycle / calcium ion transport / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / mitotic cell cycle / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / defense response to bacterium / inflammatory response / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 2.8 Å | ||||||
Authors | Tahirov, T.H. / Ogata, K. | ||||||
Citation | 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. #1: 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. #2: Journal: To be Published Title: Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / 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 | 1h88.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h88.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h88 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h88 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | OF C/EBP BETA AND MONOMER OF MYB PROTO- ONCOGENE PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 THE |
-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: RESIDUES 259-336 Source method: isolated from a genetically manipulated source Details: BZIP DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676 #2: Protein | | Mass: 19173.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-193 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DNA BINDING DOMAIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06876 |
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-DNA chain , 2 types, 2 molecules DE
#3: DNA chain | Mass: 8028.177 Da / Num. of mol.: 1 / Fragment: FRAGMENT FROM TOM-1A PROMOTER / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#4: DNA chain | Mass: 7948.129 Da / Num. of mol.: 1 / Fragment: FRAGMENT FROM TOM-1A PROMOTER / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 2 types, 26 molecules
#5: Chemical | ChemComp-NH4 / |
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#6: Water | ChemComp-HOH / |
-Details
Compound details | CHAIN C ENGINEERED MUTATION LYS47MET, ARG48GLY C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN ...CHAIN C ENGINEERED |
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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: 3.34 Å3/Da / Density % sol: 62.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M AMMONIUM ACETATE, 0.01 M MAGNESIUM CHLORIDE, 10% V/V MPD, 6% V/V GLYCEROL, 0.05 M TRIS HCL BUFFER PH 7.5 AT 24 DEGREES C | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 297 K / pH: 6.8 / Method: vapor diffusion, sitting dropDetails: Tahirov, T.H., (2001) Acta Crystallogr.,Sect.D, 57, 1655. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.97934 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 1999 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 18605 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.151 % / Biso Wilson estimate: 72.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 25.2564 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.109 / Rsym value: 0.233 / % possible all: 87.8 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Num. measured all: 56631 / Rmerge(I) obs: 0.046 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, MIR / Resolution: 2.8→19.87 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1568847.92 / 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 100
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.54 Å2 / ksol: 0.269175 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.044 / 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 Highest resolution: 2.8 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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