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- PDB-1dh3: CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FO... -
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Basic information
Entry | Database: PDB / ID: 1dh3 | ||||||
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Title | CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() AKT phosphorylates targets in the nucleus / NGF-stimulated transcription / chemotaxis to arachidonic acid / transcription coactivator binding => GO:0001223 / ATF4-CREB1 transcription factor complex / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of transforming growth factor beta3 production ...AKT phosphorylates targets in the nucleus / NGF-stimulated transcription / chemotaxis to arachidonic acid / transcription coactivator binding => GO:0001223 / ATF4-CREB1 transcription factor complex / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of transforming growth factor beta3 production / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / cAMP response element binding / NCAM signaling for neurite out-growth / secretory granule organization / : / lung saccule development / positive regulation of cardiac muscle tissue development / regulation of glial cell proliferation / lung epithelium development / : / regulation of fibroblast proliferation / pituitary gland development / response to xenobiotic stimulus => GO:0009410 / negative regulation of transcription by competitive promoter binding / positive regulation of hormone secretion / mammary gland development / positive regulation of multicellular organism growth / arrestin family protein binding / positive regulation of osteoclast differentiation / response to glucagon / cellular response to zinc ion / cellular response to insulin-like growth factor stimulus / cellular response to fatty acid / response to L-glutamate / regulation of cell size / histone acetyltransferase binding / type I pneumocyte differentiation / cellular response to hepatocyte growth factor stimulus / cellular response to platelet-derived growth factor stimulus / transcription factor binding / positive regulation of fat cell differentiation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / Hsp70 protein binding / lactation / axonogenesis / transforming growth factor beta receptor signaling pathway / : / cellular response to nerve growth factor stimulus / response to activity / cellular response to leukemia inhibitory factor / positive regulation of long-term synaptic potentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to nicotine / euchromatin / visual learning / regulation of circadian rhythm / memory / cellular response to growth factor stimulus / circadian rhythm / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / protein stabilization / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / protein phosphorylation / negative regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Goodman, R.H. / Brennan, R.G. | ||||||
![]() | ![]() Title: The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding Authors: Schumacher, M.A. / Goodman, R.H. / Brennan, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 386 KB | Display | ![]() |
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Full document | ![]() | 415.3 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6424.148 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 6686.831 Da / Num. of mol.: 2 / Fragment: RESIDUES 201-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.01 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 8000, MGCL2, (NH4)2SO4, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3→10 Å / Num. all: 7436 / Num. obs: 7316 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.258 / % possible all: 95 |
Reflection | *PLUS % possible obs: 95 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 87.4 % / Mean I/σ(I) obs: 3.6 |
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Processing
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Refinement | Resolution: 3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 Details: THE FIRST AND LAST TWO RESIDUES ARE DISORDERED AND NOT MODELED. THE DENSITY IS WEAK FOR RESIDUES 334-339 IN BOTH PROTEIN CHAINS. PROCHECK REVEALED NO BAD CONTACTS AND NO RAMACHANDRAN OUTLIERS
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |