+Open data
-Basic information
Entry | Database: PDB / ID: 2rtu | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of oxidized human HMGB1 A box | ||||||
Components | High mobility group protein B1High-mobility group | ||||||
Keywords | DNA BINDING PROTEIN / disulfide bond / High Mobility Group Box 1 | ||||||
Function / homology | Function and homology information regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / C-X-C chemokine binding / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / Regulation of TLR by endogenous ligand / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / Apoptosis induced DNA fragmentation / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / supercoiled DNA binding / MyD88 deficiency (TLR2/4) / positive regulation of monocyte chemotaxis / apoptotic cell clearance / dendritic cell chemotaxis / DNA binding, bending / IRAK4 deficiency (TLR2/4) / positive regulation of vascular endothelial cell proliferation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / phosphatidylserine binding / positive regulation of activated T cell proliferation / chemoattractant activity / negative regulation of blood vessel endothelial cell migration / TRAF6 mediated NF-kB activation / DNA topological change / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-10 production / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / Pyroptosis / DNA polymerase binding / heterochromatin formation / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / transcription repressor complex / activation of innate immune response / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / autophagy / double-strand break repair via nonhomologous end joining / positive regulation of interleukin-6 production / neuron projection development / transcription corepressor activity / integrin binding / positive regulation of tumor necrosis factor production / single-stranded DNA binding / ER-Phagosome pathway / positive regulation of cytosolic calcium ion concentration / double-stranded DNA binding / secretory granule lumen / DNA-binding transcription factor binding / DNA recombination / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / damaged DNA binding / positive regulation of viral entry into host cell / transcription coactivator activity / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / transcription cis-regulatory region binding / lyase activity / endosome / inflammatory response / positive regulation of apoptotic process / innate immune response / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular region / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Jing, W. / Tochio, N. / Tate, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA. Authors: Wang, J. / Tochio, N. / Takeuchi, A. / Uewaki, J. / Kobayashi, N. / Tate, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rtu.cif.gz | 602.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rtu.ent.gz | 514.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/2rtu ftp://data.pdbj.org/pub/pdb/validation_reports/rt/2rtu | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10118.655 Da / Num. of mol.: 1 / Fragment: HMG box 1, UNP residues 1-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09429 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 200 / pH: 6.4 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, 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: 40 / Conformers submitted total number: 20 / Representative conformer: 1 |