- PDB-4qr9: Crystal structure of two HMGB1 Box A domains cooperating to under... -
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Basic information
Entry
Database: PDB / ID: 4qr9
Title
Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA
Components
DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
High mobility group protein B1
Keywords
DNA BINDING PROTEIN / HMG-box / HMGB1 / Box A domain / High mobility group / DNA-binding / bend DNA / kink DNA / architectural factor / minor groove / chromatin / Nucleus
Function / homology
Function and homology information
Apoptosis induced DNA fragmentation / male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...Apoptosis induced DNA fragmentation / male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / plasmacytoid dendritic cell activation / TAK1-dependent IKK and NF-kappa-B activation / Regulation of TLR by endogenous ligand / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of myeloid cell differentiation / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of macrophage inflammatory protein 1 alpha production / bent DNA binding / positive regulation of dendritic cell differentiation / glycolipid binding / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of glycogen catabolic process / positive regulation of toll-like receptor 4 signaling pathway / neutrophil clearance / endothelial cell chemotaxis / positive regulation of DNA ligation / eye development / positive regulation of interleukin-1 production / RAGE receptor binding / alphav-beta3 integrin-HMGB1 complex / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / myeloid cell differentiation / myeloid progenitor cell differentiation / regulation of nucleotide-excision repair / macrophage activation involved in immune response / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / inflammatory response to antigenic stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / cellular response to interleukin-7 / glycogen catabolic process / supercoiled DNA binding / apoptotic cell clearance / myoblast proliferation / endothelial cell proliferation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / Neutrophil degranulation / positive regulation of wound healing / negative regulation of DNA replication / positive regulation of smooth muscle cell migration / protein kinase activator activity / positive regulation of sprouting angiogenesis / positive regulation of activated T cell proliferation / phosphatidylserine binding / response to type II interferon / positive regulation of interleukin-10 production / positive regulation of interferon-alpha production / negative regulation of blood vessel endothelial cell migration / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of type II interferon production / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / response to glucose / positive regulation of autophagy / DNA polymerase binding / four-way junction DNA binding / response to glucocorticoid / condensed chromosome / activation of innate immune response / positive regulation of interleukin-12 production / transcription repressor complex / positive regulation of interferon-beta production / positive regulation of mitotic cell cycle / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / lung development / peptide binding / response to insulin / cell morphogenesis / base-excision repair / heterochromatin formation Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
A: High mobility group protein B1 B: High mobility group protein B1 C: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') D: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') E: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') F: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') hetero molecules
Resolution: 2→42.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.442 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23387
1176
5 %
RANDOM
Rwork
0.19675
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-
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obs
0.19868
22219
98.78 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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