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Protein

High mobility group protein B3

Gene

Hmgb3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters (By similarity). Proposed to be involved in the innate immune response to nucleic acids by acting as a cytoplasmic promiscuous immunogenic DNA/RNA sensor (PubMed:19890330). Negatively regulates B-cell and myeloid cell differentiation. In hematopoietic stem cells may regulate the balance between self-renewal and differentiation. Involved in negative regulation of canonical Wnt signaling (PubMed:12714519, PubMed:15358624, PubMed:16945912).By similarity4 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi9 – 7971HMG box 1PROSITE-ProRule annotationAdd
BLAST
DNA bindingi93 – 16169HMG box 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • chromatin binding Source: GO_Central
  • DNA binding Source: UniProtKB
  • DNA binding, bending Source: AgBase
  • four-way junction DNA binding Source: AgBase
  • poly(A) RNA binding Source: Ensembl
  • RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Immunity, Innate immunity, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B3
Alternative name(s):
High mobility group protein 2a
Short name:
HMG-2a
High mobility group protein 4
Short name:
HMG-4
Gene namesi
Name:Hmgb3
Synonyms:Hmg2a, Hmg4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome X

Organism-specific databases

MGIiMGI:1098219. Hmgb3.

Subcellular locationi

GO - Cellular componenti

  • chromosome Source: UniProtKB-SubCell
  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 200200High mobility group protein B3PRO_0000048540Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi23 ↔ 45In disulfide HMGB3By similarity
Modified residuei23 – 231Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB3; alternateBy similarity
Modified residuei45 – 451Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB3; alternateBy similarity
Modified residuei104 – 1041Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB3; alternateBy similarity

Post-translational modificationi

Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-104 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 HMGB3 (HMGB3C23hC45hC104h), 2- disulfide HMGB3 (HMGB3C23-C45C104h) and 3- sulfonyl HMGB3 (HMGB3C23soC45soC104so).By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiO54879.
PaxDbiO54879.
PRIDEiO54879.

PTM databases

iPTMnetiO54879.
PhosphoSiteiO54879.

Expressioni

Tissue specificityi

Expressed in bone marrow cells, specifically in primitive Lin-, c-kit+, Sca-1+, IL-7Ralpha- cells, and Ter119+ erythroid cells (PubMed:12714519).1 Publication

Developmental stagei

Highly expressed in the embryo; barely detectable in the adult stage.

Gene expression databases

BgeeiO54879.
CleanExiMM_HMGB3.
ExpressionAtlasiO54879. baseline and differential.
GenevisibleiO54879. MM.

Interactioni

Protein-protein interaction databases

BioGridi200336. 1 interaction.
IntActiO54879. 1 interaction.
MINTiMINT-4097577.
STRINGi10090.ENSMUSP00000015361.

Structurei

3D structure databases

ProteinModelPortaliO54879.
SMRiO54879. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi181 – 20020Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the HMGB family.Curated
Contains 2 HMG box DNA-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiO54879.
KOiK11296.
OMAiEEWKEDD.
OrthoDBiEOG7WHHBQ.
PhylomeDBiO54879.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031077. HMGB3.
[Graphical view]
PANTHERiPTHR13711:SF144. PTHR13711:SF144. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O54879-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKGDPKKPK GKMSAYAFFV QTCREEHKKK NPEVPVNFAE FSKKCSERWK
60 70 80 90 100
TMSSKEKSKF DEMAKADKVR YDREMKDYGP AKGGKKKKDP NAPKRPPSGF
110 120 130 140 150
FLFCSEFRPK IKSTNPGISI GDVAKKLGEM WNNLSDNEKQ PYVTKAAKLK
160 170 180 190 200
EKYEKDVADY KSKGKFDGAK GPAKVARKKV EEEEEEEEEE EEEEEEEEDE
Length:200
Mass (Da):23,010
Last modified:January 23, 2007 - v3
Checksum:i34A45470D4F1B1FB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF022465 mRNA. Translation: AAC16925.1.
BC011276 mRNA. Translation: AAH11276.1.
BC083352 mRNA. Translation: AAH83352.1.
CCDSiCCDS30180.1.
RefSeqiNP_001280552.1. NM_001293623.1.
NP_001280553.1. NM_001293624.1.
NP_001280554.1. NM_001293625.1.
NP_032279.1. NM_008253.4.
XP_006527905.1. XM_006527842.2.
UniGeneiMm.336087.

Genome annotation databases

EnsembliENSMUST00000015361; ENSMUSP00000015361; ENSMUSG00000015217.
ENSMUST00000072699; ENSMUSP00000110232; ENSMUSG00000015217.
ENSMUST00000088874; ENSMUSP00000086260; ENSMUSG00000015217.
ENSMUST00000114582; ENSMUSP00000110229; ENSMUSG00000015217.
GeneIDi15354.
KEGGimmu:15354.
UCSCiuc009tkb.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF022465 mRNA. Translation: AAC16925.1.
BC011276 mRNA. Translation: AAH11276.1.
BC083352 mRNA. Translation: AAH83352.1.
CCDSiCCDS30180.1.
RefSeqiNP_001280552.1. NM_001293623.1.
NP_001280553.1. NM_001293624.1.
NP_001280554.1. NM_001293625.1.
NP_032279.1. NM_008253.4.
XP_006527905.1. XM_006527842.2.
UniGeneiMm.336087.

3D structure databases

ProteinModelPortaliO54879.
SMRiO54879. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200336. 1 interaction.
IntActiO54879. 1 interaction.
MINTiMINT-4097577.
STRINGi10090.ENSMUSP00000015361.

PTM databases

iPTMnetiO54879.
PhosphoSiteiO54879.

Proteomic databases

MaxQBiO54879.
PaxDbiO54879.
PRIDEiO54879.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000015361; ENSMUSP00000015361; ENSMUSG00000015217.
ENSMUST00000072699; ENSMUSP00000110232; ENSMUSG00000015217.
ENSMUST00000088874; ENSMUSP00000086260; ENSMUSG00000015217.
ENSMUST00000114582; ENSMUSP00000110229; ENSMUSG00000015217.
GeneIDi15354.
KEGGimmu:15354.
UCSCiuc009tkb.2. mouse.

Organism-specific databases

CTDi3149.
MGIiMGI:1098219. Hmgb3.

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiO54879.
KOiK11296.
OMAiEEWKEDD.
OrthoDBiEOG7WHHBQ.
PhylomeDBiO54879.
TreeFamiTF105371.

Miscellaneous databases

NextBioi287964.
PROiO54879.
SOURCEiSearch...

Gene expression databases

BgeeiO54879.
CleanExiMM_HMGB3.
ExpressionAtlasiO54879. baseline and differential.
GenevisibleiO54879. MM.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031077. HMGB3.
[Graphical view]
PANTHERiPTHR13711:SF144. PTHR13711:SF144. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Hmg4, a new member of the Hmg1/2 gene family."
    Vaccari T., Beltrame M., Ferrari S., Bianchi M.E.
    Genomics 49:247-252(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: 129/Sv.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Eye.
  3. "Hmgb3: an HMG-box family member expressed in primitive hematopoietic cells that inhibits myeloid and B-cell differentiation."
    Nemeth M.J., Curtis D.J., Kirby M.R., Garrett-Beal L.J., Seidel N.E., Cline A.P., Bodine D.M.
    Blood 102:1298-1306(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.
  4. "Hmgb3 deficiency deregulates proliferation and differentiation of common lymphoid and myeloid progenitors."
    Nemeth M.J., Cline A.P., Anderson S.M., Garrett-Beal L.J., Bodine D.M.
    Blood 105:627-634(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. Cited for: FUNCTION, SUBCELLULAR LOCATION.
  6. "Hmgb3 regulates the balance between hematopoietic stem cell self-renewal and differentiation."
    Nemeth M.J., Kirby M.R., Bodine D.M.
    Proc. Natl. Acad. Sci. U.S.A. 103:13783-13788(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiHMGB3_MOUSE
AccessioniPrimary (citable) accession number: O54879
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: January 23, 2007
Last modified: January 20, 2016
This is version 129 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.