[English] 日本語
Yorodumi- PDB-2yrq: Solution structure of the tandem HMG box domain from Human High m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yrq | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the tandem HMG box domain from Human High mobility group protein B1 | ||||||
Components | High mobility group protein B1High-mobility group | ||||||
Keywords | DNA BINDING PROTEIN / HMG box domain / DNA binding / Helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the tandem HMG box domain from Human High mobility group protein B1 Authors: Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yrq.cif.gz | 1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yrq.ent.gz | 924.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/2yrq ftp://data.pdbj.org/pub/pdb/validation_reports/yr/2yrq | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 19674.662 Da / Num. of mol.: 1 / Fragment: HMG box domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: HMGB1 / Plasmid: P061030-05 / References: UniProt: P09429 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.09mM HMG box domain U-15N,13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |