+Open data
-Basic information
Entry | Database: PDB / ID: 1j3c | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the C-terminal domain of the HMGB2 | ||||||
Components | High mobility group protein 2High-mobility group | ||||||
Keywords | DNA BINDING PROTEIN / HMG-BOX | ||||||
Function / homology | Function and homology information Apoptosis induced DNA fragmentation / non-sequence-specific DNA binding, bending / positive regulation of DNA ligase activity / spermatid nucleus differentiation / DNA geometric change / regulation of stem cell proliferation / inflammatory response to antigenic stimulus / supercoiled DNA binding / response to steroid hormone / DNA binding, bending ...Apoptosis induced DNA fragmentation / non-sequence-specific DNA binding, bending / positive regulation of DNA ligase activity / spermatid nucleus differentiation / DNA geometric change / regulation of stem cell proliferation / inflammatory response to antigenic stimulus / supercoiled DNA binding / response to steroid hormone / DNA binding, bending / DNA topological change / transcription factor binding / regulation of neurogenesis / positive regulation of DNA binding / cis-regulatory region sequence-specific DNA binding / four-way junction DNA binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / condensed chromosome / nucleosome assembly / double-strand break repair via nonhomologous end joining / male gonad development / chemotaxis / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / DNA recombination / defense response to Gram-negative bacterium / response to lipopolysaccharide / defense response to Gram-positive bacterium / protein domain specific binding / negative regulation of gene expression / innate immune response / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kurita, J. / Shimahara, H. / Yoshida, M. / Tate, S. | ||||||
Citation | Journal: To be Published Title: Strucutral comparison of two HMG-boxes in the non-histone protein HMG-2 with in the HMG-1 Authors: Kurita, J. / Shimahara, H. / Yoshida, M. / Tate, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j3c.cif.gz | 743.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j3c.ent.gz | 627.2 KB | Display | PDB format |
PDBx/mmJSON format | 1j3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3c ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3c | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9109.550 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, B domain / Mutation: H22Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): pET / References: UniProt: P17741 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
|
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz |
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 100 / Conformers submitted total number: 30 |