+Open data
-Basic information
Entry | Database: PDB / ID: 1nwq | ||||||
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Title | CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / BASIC LEUCINE ZIPPER / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information Transcriptional regulation of granulopoiesis / response to vitamin B2 / CHOP-C/EBP complex / response to phenylpropanoid / HMG box domain binding / Rb-E2F complex / cellular response to xenobiotic stimulus => GO:0071466 / RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / granulocyte differentiation ...Transcriptional regulation of granulopoiesis / response to vitamin B2 / CHOP-C/EBP complex / response to phenylpropanoid / HMG box domain binding / Rb-E2F complex / cellular response to xenobiotic stimulus => GO:0071466 / RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / myeloid cell differentiation / positive regulation of macrophage activation / positive regulation of transcription by RNA polymerase III / osteoblast development / interleukin-6-mediated signaling pathway / response to dexamethasone / cellular response to lithium ion / fat cell differentiation / lipid homeostasis / inner ear development / macrophage differentiation / transcription factor binding / cellular response to organic cyclic compound / white fat cell differentiation / negative regulation of cell cycle / positive regulation of fat cell differentiation / embryonic placenta development / positive regulation of osteoblast differentiation / transcription by RNA polymerase I / animal organ regeneration / brown fat cell differentiation / cell maturation / Notch signaling pathway / cholesterol metabolic process / mitochondrion organization / response to nutrient / liver development / acute-phase response / lung development / memory / nuclear matrix / kinase binding / positive regulation of inflammatory response / histone deacetylase binding / RNA polymerase II transcription regulator complex / glucose homeostasis / cellular response to tumor necrosis factor / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / protein-containing complex binding / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / 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 / protein-containing complex / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Miller, M. / Shuman, J.D. / Sebastian, T. / Dauter, Z. / Johnson, P.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/enhancer Binding Protein Alpha Authors: Miller, M. / Shuman, J.D. / Sebastian, T. / Dauter, Z. / Johnson, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nwq.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nwq.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nwq ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nwq | HTTPS FTP |
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-Related structure data
Related structure data | 1dh3S 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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Unit cell |
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-Components
#1: DNA chain | Mass: 6364.120 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6520.249 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 7428.297 Da / Num. of mol.: 2 / Fragment: BASIC REGION, LEUCINE ZIPPER DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CEBPA / Plasmid: PT5 / Production host: Escherichia coli (E. coli) / References: UniProt: P05554 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: NACL, MGCL2, PEG 400, MES, GLYCEROL, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 1.07 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 12416 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 17.8 % / Biso Wilson estimate: 78.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.7 / % possible all: 91.6 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å / Num. measured all: 222356 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 91.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DH3 Resolution: 2.8→38.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1483361.25 / Data cutoff high rms absF: 1483361.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0305 Å2 / ksol: 0.25376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→38.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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