4QR9 | pdb_00004qr9

Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HMG-box	8036763	3001368	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HMG-box	8036763	3001368	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Pkinase, APH	e4qr9A1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: Pkinase, APH	ECOD (v294.1)
B	Pkinase, APH	e4qr9B1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: Pkinase, APH	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
B	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09011	HMG-box domain (HMG_box_2)	HMG-box domain	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long ...	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, E, F	DNA (5'-D(APTPAPTPCPGPAPTPAPT)-3')	-	-	-
A, B	High mobility group protein B1	binding nucleic acid binding DNA binding double-stranded DNA binding supercoiled DNA binding DNA binding, bending non-sequence-specific DNA binding, bending DNA secondary structure binding four-way junction DNA binding bubble DNA binding crossed form four-way junction DNA binding lipid binding lipopolysaccharide binding carbohydrate derivative binding binding nucleic acid binding DNA binding double-stranded DNA binding supercoiled DNA binding DNA binding, bending non-sequence-specific DNA binding, bending DNA secondary structure binding four-way junction DNA binding bubble DNA binding crossed form four-way junction DNA binding lipid binding lipopolysaccharide binding carbohydrate derivative binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity transcription corepressor activity transcription regulator activity transcription coregulator activity transcription factor binding protein binding DNA-binding transcription factor binding calcium-dependent protein kinase regulator activity single-stranded DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA binding double-stranded RNA binding glycolipid binding open form four-way junction DNA binding modified amino acid binding ion binding anion binding phospholipid binding phosphatidylserine binding small molecule binding chemokine binding C-X-C chemokine binding cytokine binding rRNA binding 5S rRNA binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity RNA polymerase II-specific DNA-binding transcription factor binding protein heterodimerization activity protein dimerization activity transcription coactivator activity lyase activity catalytic activity single-stranded RNA binding damaged DNA binding bent DNA binding cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding cytokine activity RAGE receptor binding peptide binding DNA polymerase binding enzyme binding heparin binding glycosaminoglycan binding sulfur compound binding	response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process immune system development developmental process multicellular organism development immune system process anatomical structure development regulation of immune system process regulation of tolerance induction tolerance induction system development regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of myoblast differentiation myoblast differentiation cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of toll-like receptor 9 signaling pathway regulation of signaling positive regulation of innate immune response defense response defense response to symbiont regulation of cell communication positive regulation of signaling myoblast proliferation cell population proliferation cellular component organization organelle organization DNA geometric change chromosome organization DNA conformation change cellular component organization or biogenesis response to antibiotic catabolic process autophagy process utilizing autophagic mechanism behavior system process learning or memory nervous system process cognition memory positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of leukocyte differentiation cell development mononuclear cell differentiation regulation of cell development positive regulation of hemopoiesis regulation of multicellular organismal development hemopoiesis positive regulation of cell development regulation of dendritic cell differentiation regulation of hemopoiesis dendritic cell differentiation positive regulation of leukocyte differentiation positive regulation of dendritic cell differentiation leukocyte differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response T-helper cell differentiation cell activation T cell differentiation involved in immune response T-helper 1 type immune response adaptive immune response immune effector process T-helper 1 cell differentiation regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cell projection organization neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production response to type II interferon response to cytokine response to peptide negative regulation of transcription initiation by RNA polymerase II transcription preinitiation complex assembly negative regulation of biological process regulation of primary metabolic process negative regulation of RNA biosynthetic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of cellular component organization negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process negative regulation of protein-containing complex assembly negative regulation of macromolecule biosynthetic process RNA polymerase II preinitiation complex assembly regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly negative regulation of RNA polymerase II transcription preinitiation complex assembly RNA metabolic process protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process regulation of protein-containing complex assembly protein-containing complex assembly negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process protein-containing complex organization protein-DNA complex assembly nucleobase-containing compound biosynthetic process regulation of cellular component biogenesis DNA-templated transcription initiation nucleic acid metabolic process negative regulation of biosynthetic process regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation anatomical structure morphogenesis cell morphogenesis positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation vascular endothelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production regulation of type II interferon production type II interferon production negative regulation of type II interferon production negative regulation of cytokine production negative regulation of gene expression negative regulation of multicellular organismal process localization import into cell transport phagocytosis apoptotic cell clearance endocytosis establishment of localization vesicle-mediated transport cellular response to interleukin-1 cellular response to cytokine stimulus response to interleukin-1 positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process negative regulation of DNA replication DNA metabolic process DNA replication negative regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production chromatin organization rhythmic process circadian rhythm immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway cell surface receptor signaling pathway toll-like receptor 4 signaling pathway positive chemotaxis chemotaxis positive regulation of positive chemotaxis induction of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis regulation of positive chemotaxis taxis positive regulation of ERK1 and ERK2 cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity immune response to tumor cell regulation of response to tumor cell T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of T cell mediated immunity response to tumor cell regulation of adaptive immune response regulation of immune response to tumor cell regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of localization negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport negative regulation of apoptotic cell clearance regulation of apoptotic cell clearance regulation of myeloid cell differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation positive regulation of mesenchymal cell proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production toll-like receptor 2 signaling pathway response to hexose response to monosaccharide response to carbohydrate response to glucose response to oxygen-containing compound regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production chromatin remodeling nucleosome assembly nucleosome organization regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration blood vessel endothelial cell migration regulation of endothelial cell migration neuron apoptotic process apoptotic process cell death programmed cell death regulation of cellular response to stress cellular response to stress nucleotide-excision repair DNA repair regulation of DNA repair DNA damage response regulation of nucleotide-excision repair response to hormone response to endogenous stimulus response to peptide hormone response to insulin response to nitrogen compound heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression, epigenetic regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction regulation of sprouting angiogenesis angiogenesis regulation of vasculature development tube morphogenesis positive regulation of sprouting angiogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis sprouting angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis psychomotor behavior motor behavior myeloid dendritic cell activation myeloid leukocyte activation inflammatory response positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production response to lipid response to lipopolysaccharide response to bacterium response to molecule of bacterial origin homeostatic process neutrophil clearance neutrophil homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostasis of number of cells myeloid cell homeostasis toll-like receptor signaling pathway MyD88-dependent toll-like receptor signaling pathway positive regulation of response to wounding wound healing regulation of response to wounding positive regulation of wound healing regulation of wound healing response to wounding monosaccharide metabolic process energy derivation by oxidation of organic compounds carbohydrate catabolic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process macromolecule catabolic process positive regulation of glycogen metabolic process glucan metabolic process polysaccharide metabolic process regulation of small molecule metabolic process regulation of glycogen catabolic process glycogen catabolic process small molecule metabolic process positive regulation of glycogen catabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process carbohydrate metabolic process regulation of carbohydrate catabolic process glucan catabolic process glycogen metabolic process hexose metabolic process generation of precursor metabolites and energy positive regulation of glucose metabolic process polysaccharide catabolic process energy reserve metabolic process positive regulation of carbohydrate metabolic process positive regulation of small molecule metabolic process regulation of glycogen metabolic process glucose metabolic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process myeloid cell apoptotic process positive regulation of myeloid cell apoptotic process regulation of myeloid cell apoptotic process actin cytoskeleton organization actin filament-based process cytoskeleton organization regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production regulation of chemokine production chemokine production positive regulation of chemokine production positive regulation of JNK cascade JNK cascade regulation of JNK cascade macrophage activation involved in immune response myeloid cell activation involved in immune response macrophage activation negative regulation of locomotion negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration negative regulation of cell motility negative regulation of cell migration inflammatory response to antigenic stimulus positive regulation of monocyte chemotaxis regulation of monocyte chemotaxis myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of mononuclear cell migration cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis monocyte chemotaxis leukocyte migration cellular response to chemical stimulus mononuclear cell migration leukocyte chemotaxis base-excision repair mismatch repair positive regulation of mismatch repair positive regulation of DNA repair positive regulation of DNA metabolic process regulation of mismatch repair positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of myeloid progenitor cell differentiation positive regulation of myeloid progenitor cell differentiation myeloid progenitor cell differentiation regulation of hematopoietic progenitor cell differentiation positive regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production positive regulation of macrophage inflammatory protein 1 alpha production positive regulation of cytosolic calcium ion concentration regulation of biological quality endothelial cell chemotaxis plasmacytoid dendritic cell activation interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production regulation of toll-like receptor 2 signaling pathway positive regulation of toll-like receptor 2 signaling pathway animal organ development respiratory tube development lung development respiratory system development cellular response to lipopolysaccharide cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to lipid regulation of monocyte chemotactic protein-1 production positive regulation of monocyte chemotactic protein-1 production monocyte chemotactic protein-1 production response to corticosteroid response to steroid hormone response to glucocorticoid regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion negative regulation of cell differentiation regulation of cell-cell adhesion regulation of lymphocyte differentiation negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of immune system process negative regulation of alpha-beta T cell activation regulation of lymphocyte activation response to alcohol response to ethanol positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of activated T cell proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation activated T cell proliferation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of T cell proliferation regulation of mononuclear cell proliferation sensory organ development eye development visual system development sensory system development T-helper 1 cell activation double-strand break repair defense response to bacterium male-specific defense response to bacterium response to interleukin-7 cellular response to interleukin-7 double-strand break repair via nonhomologous end joining somatic cell DNA recombination DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-HMGB1 complex cell surface membrane microdomain membrane raft cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-HMGB1 complex cell surface membrane microdomain membrane raft intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome cell projection neuron projection plasma membrane bounded cell projection membrane-bounded organelle endoplasmic reticulum-Golgi intermediate compartment intracellular membrane-bounded organelle condensed chromosome early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle transcription regulator complex transcription repressor complex nucleus endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
A, B	IPR050342	High Mobility Group Box (HMGB)	Family
A, B	IPR017967	HMG box A DNA-binding domain, conserved site	Conserved Site
A, B	IPR009071	High mobility group box domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.