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High mobility group protein B1



Rattus norvegicus (Rat)
Reviewed-Annotation score: -Experimental evidence at protein leveli


Multifunctional redox sensitive protein with various roles in different cellular compartments. In the nucleus is one of the major chromatin-associated non-histone proteins and acts as a DNA chaperone involved in replication, transcription, chromatin remodeling, V(D)J recombination, DNA repair and genome stability. Proposed to be an universal biosensor for nucleic acids. Promotes host inflammatory response to sterile and infectious signals and is involved in the coordination and integration of innate and adaptive immune responses. In the cytoplasm functions as sensor and/or chaperone for immunogenic nucleic acids implicating the activation of TLR9-mediated immune responses, and mediates autophagy. Acts as danger associated molecular pattern (DAMP) molecule that amplifies immune responses during tissue injury. Released to the extracellular environment can bind DNA, nucleosomes, IL-1 beta, CXCL12, AGER isoform 2/sRAGE, lipopolysaccharide (LPS) and lipoteichoic acid (LTA), and activates cells through engagement of multiple surface receptors. In the extracellular compartment fully reduced HMGB1 (released by necrosis) acts as a chemokine, disulfide HMGB1 (actively secreted) as a cytokine, and sulfonyl HMGB1 (released from apoptotic cells) promotes immunological tolerance (PubMed:23519706, PubMed:23446148, PubMed:23994764, PubMed:25048472). Has proangiogenic activity. May be involved in platelet activation. Binds to phosphatidylserine and phosphatidylethanolamide (PubMed:11154118). Bound to RAGE mediates signaling for neuronal outgrowth (PubMed:1885601, PubMed:2461949, PubMed:7592757, PubMed:12183440). May play a role in accumulation of expanded polyglutamine (polyQ) proteins.By similarity4 Publications5 Publications
Nuclear functions are attributed to fully reduced HGMB1. Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA, DNA-containing cruciforms or bent structures, supercoiled DNA and ZDNA (PubMed:2922595, PubMed:11513603). Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters by enhancing transcription factor binding and/or bringing distant regulatory sequences into close proximity (PubMed:12486007). May be involved in nucleotide excision repair (NER), mismatch repair (MMR) and base excision repair (BER) pathways, and double strand break repair such as non-homologous end joining (NHEJ) (PubMed:10866811). Involved in V(D)J recombination by acting as a cofactor of the RAG complex: acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS) (By similarity). In vitro can displace histone H1 from highly bent DNA (PubMed:24551219). Can restructure the canonical nucleosome leading to relaxation of structural constraints for transcription factor-binding (By similarity). Enhances binding of sterol regulatory element-binding proteins (SREBPs) such as SREBF1 to their cognate DNA sequences and increases their transcriptional activities (By similarity). Facilitates binding of TP53 to DNA (By similarity). May be involved in mitochondrial quality control and autophagy in a transcription-dependent fashion implicating HSPB1 (By similarity). Can modulate the activity of the telomerase complex and may be involved in telomere maintenance (By similarity).By similarity5 Publications
In the cytoplasm proposed to dissociate the BECN1:BCL2 complex via competitive interaction with BECN1 leading to autophagy activation (By similarity). Can protect BECN1 and ATG5 from calpain-mediated cleavage and thus proposed to control their proautophagic and proapoptotic functions and to regulate the extent and severity of inflammation-associated cellular injury (By similarity). In myeloid cells has a protective role against endotoxemia and bacterial infection by promoting autophagy (By similarity). Involved in endosomal translocation and activation of TLR9 in response to CpG-DNA in macrophages (By similarity).By similarity
In the extracellular compartment (following either active secretion or passive release) involved in regulation of the inflammatory response. Fully reduced HGMB1 (which subsequently gets oxidized after release) in association with CXCL12 mediates the recruitment of inflammatory cells during the initial phase of tissue injury; the CXCL12:HMGB1 complex triggers CXCR4 homodimerization (PubMed:22869893). Induces the migration of monocyte-derived immature dendritic cells and seems to regulate adhesive and migratory functions of neutrophils implicating AGER/RAGE and ITGAM (By similarity). Can bind to various types of DNA and RNA including microbial unmethylated CpG-DNA to enhance the innate immune response to nucleic acids. Proposed to act in promiscuous DNA/RNA sensing which cooperates with subsequent discriminative sensing by specific pattern recognition receptors. Promotes extracellular DNA-induced AIM2 inflammasome activation implicating AGER/RAGE (By similarity). Disulfide HMGB1 binds to transmembrane receptors, such as AGER/RAGE, TLR2, TLR4 and probably TREM1, thus activating their signal transduction pathways. Mediates the release of cytokines/chemokines such as TNF, IL-1, IL-6, IL-8, CCL2, CCL3, CCL4 and CXCL10 (PubMed:10952726, PubMed:20547845, PubMed:22869893). Promotes secretion of interferon-gamma by macrophage-stimulated natural killer (NK) cells in concert with other cytokines like IL-2 or IL-12. TLR4 is proposed to be the primary receptor promoting macrophage activation and signaling through TLR4 seems to implicate LY96/MD-2 (By similarity). In bacterial LPS- or LTA-mediated inflammatory responses binds to the endotoxins and transfers them to CD14 for signaling to the respective TLR4:LY96 and TLR2 complexes (PubMed:23508573). Contributes to tumor proliferation by association with ACER/RAGE (PubMed:10830965). Can bind to IL1-beta and signals through the IL1R1:IL1RAP receptor complex (By similarity). Binding to class A CpG activates cytokine production in plasmacytoid dendritic cells implicating TLR9, MYD88 and AGER/RAGE and can activate autoreactive B cells (By similarity). Via HMGB1-containing chromatin immune complexes may also promote B cell responses to endogenous TLR9 ligands through a B-cell receptor (BCR)-dependent and ACER/RAGE-independent mechanism (By similarity). Inhibits phagocytosis of apoptotic cells by macrophages; the function is dependent on poly-ADP-ribosylation and involves binding to phosphatidylserine on the cell surface of apoptotic cells (By similarity). In adaptive immunity may be involved in enhancing immunity through activation of effector T-cells and suppression of regulatory T (TReg) cells (By similarity). In contrast, without implicating effector or regulatory T-cells, required for tumor infiltration and activation of T-cells expressing the lymphotoxin LTA:LTB heterotrimer thus promoting tumor malignant progression (By similarity). Also reported to limit proliferation of T-cells (PubMed:18277947). Released HMGB1:nucleosome complexes formed during apoptosis can signal through TLR2 to induce cytokine production. Involved in induction of immunological tolerance by apoptotic cells; its pro-inflammatory activities when released by apoptotic cells are neutralized by reactive oxygen species (ROS)-dependent oxidation specifically on Cys-106 (By similarity). During macrophage activation by activated lymphocyte-derived self apoptotic DNA (ALD-DNA) promotes recruitment of ALD-DNA to endosomes (By similarity).By similarity4 Publications


Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi9 – 79HMG box 1PROSITE-ProRule annotationAdd BLAST71
DNA bindingi95 – 163HMG box 2PROSITE-ProRule annotationAdd BLAST69

GO - Molecular functioni

  • 5S rRNA binding Source: RGD
  • bent DNA binding Source: MGI
  • bubble DNA binding Source: AgBase
  • crossed form four-way junction DNA binding Source: MGI
  • cytokine activity Source: UniProtKB
  • DNA binding, bending Source: RGD
  • double-stranded DNA binding Source: RGD
  • four-way junction DNA binding Source: RGD
  • glycolipid binding Source: RGD
  • heparin binding Source: RGD
  • open form four-way junction DNA binding Source: MGI
  • peptide binding Source: RGD
  • protein dimerization activity Source: RGD
  • RAGE receptor binding Source: RGD
  • single-stranded DNA binding Source: RGD
  • supercoiled DNA binding Source: AgBase
  • transcription factor binding Source: RGD

GO - Biological processi

  • actin cytoskeleton reorganization Source: RGD
  • adaptive immune response Source: UniProtKB-KW
  • apoptotic cell clearance Source: UniProtKB
  • autophagy Source: UniProtKB-KW
  • cell morphogenesis Source: RGD
  • cellular response to interleukin-1 Source: RGD
  • chemotaxis Source: RGD
  • circadian rhythm Source: RGD
  • DNA geometric change Source: MGI
  • DNA recombination Source: UniProtKB-KW
  • DNA repair Source: UniProtKB-KW
  • induction of positive chemotaxis Source: MGI
  • inflammatory response Source: UniProtKB-KW
  • male-specific defense response to bacterium Source: RGD
  • myoblast proliferation Source: RGD
  • negative regulation of DNA replication Source: RGD
  • nervous system development Source: RGD
  • neuron projection development Source: UniProtKB
  • neutrophil clearance Source: UniProtKB
  • positive regulation of apoptotic process Source: RGD
  • positive regulation of autophagy Source: RGD
  • positive regulation of cell death Source: RGD
  • positive regulation of cell migration Source: MGI
  • positive regulation of cell proliferation Source: RGD
  • positive regulation of DNA ligation Source: UniProtKB
  • positive regulation of interleukin-1 production Source: UniProtKB
  • positive regulation of interleukin-6 production Source: UniProtKB
  • positive regulation of interleukin-8 production Source: UniProtKB
  • positive regulation of macrophage inflammatory protein 1 alpha production Source: UniProtKB
  • positive regulation of mesenchymal cell proliferation Source: MGI
  • positive regulation of mitotic cell cycle Source: MGI
  • positive regulation of myeloid cell apoptotic process Source: RGD
  • positive regulation of myoblast differentiation Source: RGD
  • positive regulation of neuron projection development Source: RGD
  • positive regulation of smooth muscle cell migration Source: RGD
  • positive regulation of toll-like receptor 9 signaling pathway Source: UniProtKB
  • positive regulation of tumor necrosis factor production Source: UniProtKB
  • regulation of inflammatory response Source: RGD
  • regulation of T cell mediated immune response to tumor cell Source: UniProtKB
  • response to drug Source: RGD
  • response to glucose Source: RGD
  • response to heat Source: RGD
  • response to insulin Source: RGD
  • response to interferon-gamma Source: RGD
  • response to lipopolysaccharide Source: RGD


Molecular functionDNA-binding, Heparin-binding
Biological processAdaptive immunity, Autophagy, Chemotaxis, DNA damage, DNA recombination, DNA repair, Immunity, Inflammatory response, Innate immunity

Protein family/group databases


Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B1
Alternative name(s):
Heparin-binding protein p30
High mobility group protein 1
Short name:
Gene namesi
Synonyms:Hmg-1, Hmg1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi2802 Hmgb1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Chromosome, Cytoplasm, Endosome, Membrane, Nucleus, Secreted

Pathology & Biotechi


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi23C → S: No effect on nuclear localization. Decreases interaction with BCN1 and impairs in autophagy induction. Abolishes cytokine-stimulating activity and no effect on chemoattractant activity; when associated with S-45. 3 Publications1
Mutagenesisi28 – 30KKK → AAA: Partial cytoplasmic localization; when associated with 181-A--A-183. 1 Publication3
Mutagenesisi28 – 30KKK → QQQ: Partial cytoplasmic localization (mimicks acetylation); when associated with 181-Q--Q-183. 1 Publication3
Mutagenesisi38F → A: Disrupts association with chromatin; when associated A-103 and A-122. 1 Publication1
Mutagenesisi45C → A: Reduces TNF-stimulating activity. 1 Publication1
Mutagenesisi45C → S: No effect on nuclear localization. Decreases interaction with BCN1 and impairs autophagy induction. Abolishes cytokine-stimulating activity and no effect on chemoattractant activity; when associated with S-23. 3 Publications1
Mutagenesisi103F → A: Disrupts association with chromatin; when associated A-38 and A-122. 1 Publication1
Mutagenesisi106C → A: Disrupts interaction with TLR4:LY96 receptor complex and abolishes TNF release from macrophages. 1 Publication1
Mutagenesisi106C → S: Abolishes cytokine-stimulating activity; no effect on chemoattractant activity; impaired nuclear and enhanced cytoplasmic localization, retained activity in autophagy regulation. 3 Publications1
Mutagenesisi122I → A: Disrupts association with chromatin; when associated A-38 and A-103. 1 Publication1
Mutagenesisi182 – 184KKK → AAA: Partial cytoplasmic localization; when associated with 27-A--A-29. 1 Publication3
Mutagenesisi182 – 184KKK → QQQ: Partial cytoplasmic localization (mimicks acetylation); when associated with 27-Q--Q-29. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000485302 – 215High mobility group protein B1Add BLAST214

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3N6-acetyllysine1 Publication1
Modified residuei7N6-acetyllysineBy similarity1
Modified residuei8N6-acetyllysineBy similarity1
Modified residuei12N6-acetyllysineBy similarity1
Disulfide bondi23 ↔ 45In disulfide HMGB1; alternate3 Publications
Modified residuei23Cysteine sulfonic acid (-SO3H); alternate1 Publication1
Modified residuei28N6-acetyllysineBy similarity1
Modified residuei29N6-acetyllysineBy similarity1
Modified residuei30N6-acetyllysineBy similarity1
Modified residuei35PhosphoserineBy similarity1
Modified residuei43N6-acetyllysineBy similarity1
Modified residuei45Cysteine sulfonic acid (-SO3H); alternate1 Publication1
Modified residuei90N6-acetyllysineBy similarity1
Modified residuei100PhosphoserineBy similarity1
Modified residuei106Cysteine sulfonic acid (-SO3H)1 Publication1
Modified residuei127N6-acetyllysineBy similarity1
Modified residuei128N6-acetyllysineBy similarity1
Modified residuei141N6-acetyllysineBy similarity1
Modified residuei172N6-acetyllysineBy similarity1
Modified residuei173N6-acetyllysineBy similarity1
Modified residuei177N6-acetyllysineBy similarity1
Modified residuei180N6-acetyllysineBy similarity1
Modified residuei181ADP-ribosylserineBy similarity1
Modified residuei182N6-acetyllysineBy similarity1
Modified residuei183N6-acetyllysineBy similarity1
Modified residuei184N6-acetyllysineBy similarity1
Modified residuei185N6-acetyllysineBy similarity1

Post-translational modificationi

Phosphorylated at serine residues. Phosphorylation in both NLS regions is required for cytoplasmic translocation followed by secretion.By similarity
Acetylated on multiple sites upon stimulation with LPS (By similarity). Acetylation on lysine residues in the nuclear localization signals (NLS 1 and NLS 2) leads to cytoplasmic localization and subsequent secretion (PubMed:14532127). Acetylation on Lys-3 results in preferential binding to DNA ends and impairs DNA bending activity (PubMed:17269659).By similarity2 Publications
Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities in various cellular compartments: 1- fully reduced HMGB1 (HMGB1C23hC45hC106h), 2- disulfide HMGB1 (HMGB1C23-C45C106h) and 3- sulfonyl HMGB1 (HMGB1C23soC45soC106so).Curated4 Publications
Poly-ADP-ribosylated by PARP1 when secreted following stimulation with LPS.By similarity
In vitro cleavage by CASP1 is liberating a HMG box 1-containing peptide which may mediate immunogenic activity; the peptide antagonizes apoptosis-induced immune tolerance. Can be proteolytically cleaved by a thrombin:thrombomodulin complex; reduces binding to heparin and proinflammatory activities (By similarity).By similarity


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei10 – 11Cleavage; by thrombin:thrombomodulinBy similarity2
Sitei67 – 68Cleavage; by CASP1By similarity2

Keywords - PTMi

Acetylation, ADP-ribosylation, Disulfide bond, Oxidation, Phosphoprotein

Proteomic databases


PTM databases



Subunit structurei

Interacts (fully reduced HMGB1) with CXCL12; probably in a 1:2 ratio involving two molecules of CXCL12, each interacting with one HMG box of HMGB1; inhibited by glycyrrhizin (PubMed:22869893). Associates with the TLR4:LY96 receptor complex (PubMed:20547845). Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2 (By similarity). Interacts (in cytoplasm upon starvation) with BECN1; inhibits the interaction of BECN1 and BCL2 leading to promotion of autophagy (PubMed:20819940). Interacts with KPNA1; involved in nuclear import (By similarity). Interacts with AGER (PubMed:12183440). Interacts with PTPRZ1 isoform 3/phosphacan (PubMed:9507007). Interacts with SREBF1, TLR2, TLR4, TLR9, APEX1, FEN1, POLB, TERT, IL1B, MSH2, XPA, XPC, HNF1A, TP53 (By similarity). Interacts with CD24; the probable CD24:SIGLEC10 complex is proposed to inhibit HGMB1-mediated tissue damage immune response. Interacts with THBD; prevents HGMB1 interaction with ACER/RAGE and inhibits HGMB1 proinflammatory activity. Interacts with HAVCR2; impairs HMGB1 binding to B-DNA and likely HMGB1-mediated innate immume response (By similarity). Interacts with XPO1; mediating nuclear export (PubMed:14532127).By similarity5 Publications

GO - Molecular functioni

  • cytokine activity Source: UniProtKB
  • protein dimerization activity Source: RGD
  • RAGE receptor binding Source: RGD
  • transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi247493, 7 interactors
IntActiP63159, 2 interactors


Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi15 – 30Combined sources16
Turni32 – 34Combined sources3
Helixi38 – 51Combined sources14
Helixi54 – 76Combined sources23
Helixi86 – 88Combined sources3
Helixi103 – 116Combined sources14
Helixi122 – 135Combined sources14
Helixi138 – 140Combined sources3
Helixi142 – 159Combined sources18

3D structure databases


Miscellaneous databases


Family & Domainsi


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 97Sufficient for interaction with HAVCR2By similarityAdd BLAST96
Regioni2 – 10Heparin-bindingBy similarity9
Regioni3 – 15LPS binding (delipidated)By similarityAdd BLAST13
Regioni80 – 96LPS binding (Lipid A)By similarityAdd BLAST17
Regioni89 – 108Cytokine-stimulating activityBy similarityAdd BLAST20
Regioni150 – 183Binding to AGER/RAGE1 PublicationAdd BLAST34


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi27 – 43Nuclear localization signal (NLS) 11 PublicationAdd BLAST17
Motifi178 – 184Nuclear localization signal (NLS) 21 Publication7

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi186 – 215Asp/Glu-rich (acidic)Add BLAST30


The acidic C-terminal domain forms a flexible structure which can reversibly interact intramolecularily with the HMG boxes and modulate binding to DNA and other proteins.2 Publications

Sequence similaritiesi

Belongs to the HMGB family.Curated

Keywords - Domaini


Phylogenomic databases

eggNOGiKOG0381 Eukaryota

Family and domain databases

Gene3Di1.10.30.10, 2 hits
InterProiView protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
IPR017967 HMG_boxA_CS
PfamiView protein in Pfam
PF00505 HMG_box, 1 hit
PF09011 HMG_box_2, 1 hit
SMARTiView protein in SMART
SM00398 HMG, 2 hits
SUPFAMiSSF47095 SSF47095, 2 hits
PROSITEiView protein in PROSITE
PS00353 HMG_BOX_1, 1 hit
PS50118 HMG_BOX_2, 2 hits


Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P63159-1 [UniParc]FASTAAdd to basket

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Mass (Da):24,894
Last modified:January 23, 2007 - v2

Sequence databases

Select the link destinations:
Links Updated
M64986 mRNA Translation: AAA40729.1
Y00463 mRNA Translation: CAA68526.1
AF275734 mRNA Translation: AAF82799.1
BC061779 mRNA Translation: AAH61779.1
BC081839 mRNA Translation: AAH81839.1
BC088402 mRNA Translation: AAH88402.1
RefSeqiNP_037095.1, NM_012963.2

Genome annotation databases


Similar proteinsi

Entry informationi

Entry nameiHMGB1_RAT
AccessioniPrimary (citable) accession number: P63159
Secondary accession number(s): P07155
, P27109, P27428, Q548R9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 137 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program


Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome


  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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