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- PDB-2ql2: Crystal Structure of the basic-helix-loop-helix domains of the he... -
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Basic information
Entry | Database: PDB / ID: 2ql2 | ||||||
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Title | Crystal Structure of the basic-helix-loop-helix domains of the heterodimer E47/NeuroD1 bound to DNA | ||||||
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![]() | transcription/DNA / basic-helix-loop-helix / protein-DNA complex / heterodimer / DNA-binding / Activator / Developmental protein / Differentiation / Neurogenesis / Nucleus / Phosphorylation / Transcription / Transcription regulation / Cytoplasm / Phosphoprotein / transcription-DNA COMPLEX | ||||||
Function / homology | ![]() pancreatic A cell fate commitment / pancreatic PP cell fate commitment / regulation of intestinal epithelial structure maintenance / regulation of cell cycle => GO:0051726 / enteroendocrine cell differentiation / negative regulation of type B pancreatic cell apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / amacrine cell differentiation / embryonic organ morphogenesis / bHLH transcription factor binding ...pancreatic A cell fate commitment / pancreatic PP cell fate commitment / regulation of intestinal epithelial structure maintenance / regulation of cell cycle => GO:0051726 / enteroendocrine cell differentiation / negative regulation of type B pancreatic cell apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / amacrine cell differentiation / embryonic organ morphogenesis / bHLH transcription factor binding / cell development / lymphocyte differentiation / response to xenobiotic stimulus => GO:0009410 / natural killer cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / hindbrain development / endocrine pancreas development / immunoglobulin V(D)J recombination / Peyer's patch development / negative regulation of receptor signaling pathway via JAK-STAT / Myogenesis / dentate gyrus development / signal transduction involved in regulation of gene expression / positive regulation of transcription regulatory region DNA binding / camera-type eye development / insulin secretion / nucleocytoplasmic transport / anterior/posterior pattern specification / regulation of neuron differentiation / B cell lineage commitment / E-box binding / regulation of G1/S transition of mitotic cell cycle / inner ear development / transcription factor binding / neuron development / cell fate commitment / nitric oxide mediated signal transduction / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / response to glucose / positive regulation of B cell proliferation / gastrulation / positive regulation of neuron differentiation / cerebellum development / erythrocyte differentiation / PDZ domain binding / positive regulation of cell differentiation / cellular response to glucose stimulus / positive regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulator complex / nucleosome / sequence-specific double-stranded DNA binding / glucose homeostasis / nervous system development / gene expression / T cell differentiation in thymus / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / response to lipopolysaccharide / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rose, R.B. / Longo, A. / Guanga, G.P. | ||||||
![]() | ![]() Title: Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition. Authors: Longo, A. / Guanga, G.P. / Rose, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 67.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.5 KB | Display | ![]() |
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Full document | ![]() | 490.4 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mdyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a heterodimer of E47 and NeuroD1 bound to a DNA duplex. There are 2 of these complexes in the asymmetric unit. |
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Components
#1: Protein | Mass: 7141.364 Da / Num. of mol.: 2 / Fragment: basic-helix-loop-helix domain Source method: isolated from a genetically manipulated source Details: pancreatic beta cells / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 6986.231 Da / Num. of mol.: 2 / Fragment: basic helix-loop-helix domain Source method: isolated from a genetically manipulated source Details: pancreatic beta cells / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: DNA chain | Mass: 4865.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized oligonucleotide #4: DNA chain | Mass: 4932.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized oligonucleotide #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN IN CHAINS A AND C MATCH THE UNP SEQUENCE DATABASE REFERENCE P15806(ISOFORM E47; P15806- ...THE PROTEIN IN CHAINS A AND C MATCH THE UNP SEQUENCE DATABASE REFERENCE P15806(ISOFORM E47; P15806-2), RESIDUES 544-603 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 7.6 Details: 0.1 mM Imidazole, 0.2 M ammonium citrate dibasic, and 22 % PEG 4000, pH 7.6, EVAPORATION, temperature 291K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2006 Details: sagittal focusing crystal and vertical focusing double mirror |
Radiation | Monochromator: SI (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→169.546 Å / Num. obs: 18832 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1 / Num. measured all: 18434 / Num. unique all: 2594 / Rsym value: 0.77 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1MDY Resolution: 2.5→55.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: optimal B-restraints weight (rweight) in CNS was 0.0198
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Solvent computation | Bsol: 83.749 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.998 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→55.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Xplor file |
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