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- PDB-2ld5: Solution NMR-derived complex structure of Hoxa13 DNA binding doma... -
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Basic information
Entry | Database: PDB / ID: 2ld5 | ||||||
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Title | Solution NMR-derived complex structure of Hoxa13 DNA binding domain bound to DNA | ||||||
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![]() | TRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / regulation of BMP signaling pathway / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / male genitalia development / tissue homeostasis / embryonic forelimb morphogenesis / intermediate filament cytoskeleton / ventricular septum development ...endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / regulation of BMP signaling pathway / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / male genitalia development / tissue homeostasis / embryonic forelimb morphogenesis / intermediate filament cytoskeleton / ventricular septum development / artery morphogenesis / inner ear development / anatomical structure morphogenesis / vasculogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of mitotic nuclear division / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Zhang, Y. | ||||||
![]() | ![]() Title: Structural basis for sequence specific DNA binding and protein dimerization of HOXA13. Authors: Zhang, Y. / Larsen, C.A. / Stadler, H.S. / Ames, J.B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.5 KB | Display | ![]() |
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PDB format | ![]() | 238.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 573 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 8670.194 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding residues 320-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3334.239 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3369.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 1H-13C NOESY |
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Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O Solvent system: 100% D2O |
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Sample | Conc.: 0.5 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.025 / pH: 6.0 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |