+Open data
-Basic information
Entry | Database: PDB / ID: 1ci6 | ||||||
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Title | TRANSCRIPTION FACTOR ATF4-C/EBP BETA BZIP HETERODIMER | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / BZIP | ||||||
Function / homology | Function and homology information : / : / L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / : / : / HRI-mediated signaling / : / Lewy body core ...: / : / L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / : / : / HRI-mediated signaling / : / Lewy body core / : / ATF4-CREB1 transcription factor complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / positive regulation of biomineral tissue development / leucine zipper domain binding / integrated stress response signaling / Senescence-Associated Secretory Phenotype (SASP) / T-helper 1 cell activation / cAMP response element binding protein binding / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / hepatocyte proliferation / PERK-mediated unfolded protein response / PERK regulates gene expression / lens fiber cell morphogenesis / ATF4 activates genes in response to endoplasmic reticulum stress / chromatin => GO:0000785 / regulation of osteoclast differentiation / nuclear glucocorticoid receptor binding / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / cellular response to dopamine / regulation of dendritic cell differentiation / negative regulation of cold-induced thermogenesis / regulation of interleukin-6 production / embryonic hemopoiesis / mammary gland epithelial cell proliferation / microtubule organizing center / regulation of osteoblast differentiation / histone acetyltransferase binding / positive regulation of interleukin-4 production / positive regulation of transcription by RNA polymerase I / fat cell differentiation / bone mineralization / ubiquitin-like protein ligase binding / transcription factor binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to organic cyclic compound / positive regulation of vascular endothelial growth factor production / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interleukin-1 / cellular response to glucose starvation / positive regulation of osteoblast differentiation / brown fat cell differentiation / negative regulation of T cell proliferation / ovarian follicle development / endoplasmic reticulum unfolded protein response / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to nutrient levels / nuclear periphery / gluconeogenesis / liver regeneration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / neuron differentiation / memory / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / positive regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to UV / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription by RNA polymerase II / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / defense response to bacterium / neuron projection Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Podust, L.M. / Kim, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of the CCAAT box/enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA Authors: Podust, L.M. / Krezel, A.M. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ci6.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ci6.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ci6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ci6_validation.pdf.gz | 384 KB | Display | wwPDB validaton report |
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Full document | 1ci6_full_validation.pdf.gz | 383.6 KB | Display | |
Data in XML | 1ci6_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1ci6_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1ci6 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1ci6 | HTTPS FTP |
-Related structure data
Related structure data | 1fosS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7471.692 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P18848 | ||||
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#2: Protein | Mass: 7746.054 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P28033 | ||||
#3: Chemical | #4: Chemical | ChemComp-BME / | #5: 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: 3.5 Å3/Da / Density % sol: 64.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0 M (NH4)2SO4, 100 MM SODIUM CACODYLATE, PH 6.5, 10.0 % DIOXANE AT 15 DEGREES C, VAPOR DIFFUSION, HANGING DROP, temperature 288K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 6800 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.082 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.48 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 58744 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FOS Resolution: 2.6→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 303496.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 87.74 Å2 / ksol: 0.48 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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