+Open data
-Basic information
Entry | Database: PDB / ID: 1h8a | ||||||
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Title | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION REGULATION / BZIP / V-MYB / C-MYB / AMV / C/EBP / AVIAN MYELOBLASTOSIS VIRUS / TRANSFORMING PROTEIN / TRANSCRIPTION-DNA complex | ||||||
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 biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / embryonic placenta development / histone acetyltransferase binding / positive regulation of fat cell differentiation / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / liver regeneration / response to endoplasmic reticulum stress / cellular response to amino acid stimulus / acute-phase response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / neuron differentiation / chromatin DNA binding / RNA polymerase II transcription regulator complex / histone deacetylase binding / nuclear matrix / positive regulation of inflammatory response / sequence-specific double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / transcription cis-regulatory region binding / transcription by RNA polymerase II / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / immune response / DNA-binding transcription factor activity / host cell nucleus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) AVIAN MYELOBLASTOSIS VIRUS Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8a.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8a.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8a_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 1h8a_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 1h8a_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1h8a_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8a ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8a | HTTPS FTP |
-Related structure data
Related structure data | 1h88SC 1h89C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 TRANSFORMING PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350. |
-Components
#1: Protein | Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: RESIDUES 259-336 Source method: isolated from a genetically manipulated source 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: 15483.731 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AVIAN MYELOBLASTOSIS VIRUS / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01104 #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) #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) #5: Water | ChemComp-HOH / | Compound details | C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND ...C/EBP BETA IS IMPORTANT TRANSCRIPT | Sequence details | NUMBERING OF AMV V-MYB AMINO ACID SEQUENCE WAS CHANGED IN ORDER TO MAKE THE COMPARISON WITH ...NUMBERING OF AMV V-MYB AMINO ACID SEQUENCE WAS CHANGED IN ORDER TO MAKE THE COMPARISON | |
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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: 3.61 Å3/Da / Density % sol: 65 % Description: LEUCINE ZIPPER OF C/EBP BETA AND C-MYB REPEAT 1 WERE EXCLUDED FROM STARTING MODEL. | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.04 M MAGNESIUM CHLORIDE, 20% V/V MPD, 0.05 M SODIUM CACODYLATE BUFFER PH 6.0 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: 1.02 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 1999 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 42104 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.868 % / Biso Wilson estimate: 67.5 Å2 / Rsym value: 0.069 / Net I/σ(I): 23.9495 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.56 % / Mean I/σ(I) obs: 1.784 / Rsym value: 0.389 / % possible all: 94.2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Num. measured all: 162864 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS Redundancy: 2.56 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H88 Resolution: 2.23→19.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2363401.12 / 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 20 TWO DATA SETS WERE COLLECTED FROM ONE CRYSTAL. FIRST ...Details: BULK SOLVENT MODEL USED. ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 20 TWO DATA SETS WERE COLLECTED FROM ONE CRYSTAL. FIRST 120 IMAGES WERE OBTAINED WITH EXPOSURE TIME OF 200 SEC, OSCILLATION ANGLE OF 1 DEGREE AND CRYSTAL TO DETECTOR DISTANCE OF 240 MM. ANOTHER 60 IMAGES WERE OBTAINED WITH EXPOSURE TIME OF 30 SEC, OSCILLATION ANGLE OF 1.5 DEGREES AND CRYSTAL TO DETECTOR DISTANCE OF 420 MM.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2952 Å2 / ksol: 0.282507 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.23→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.37 Å / Rfactor Rfree error: 0.023 / 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 Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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