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Protein

High mobility group protein B3

Gene

HMGB3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 (By similarity). 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 (By similarity).By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi9 – 79HMG box 1PROSITE-ProRule annotationAdd BLAST71
DNA bindingi93 – 161HMG box 2PROSITE-ProRule annotationAdd BLAST69

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding
Biological processImmunity, Innate immunity, Transcription, Transcription regulation

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000029993.14
HGNCiHGNC:5004 HMGB3
MIMi300193 gene
neXtProtiNX_O15347

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

Chromosome, Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Microphthalmia, syndromic, 13 (MCOPS13)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of microphthalmia, a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. MCOPS13 patients exhibit colobomatous microphthalmia with microcephaly, short stature, and psychomotor retardation.
See also OMIM:300915

Keywords - Diseasei

Microphthalmia

Organism-specific databases

DisGeNETi3149
MalaCardsiHMGB3
MIMi300915 phenotype
OpenTargetsiENSG00000029993
PharmGKBiPA35092

Polymorphism and mutation databases

BioMutaiHMGB3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000485391 – 200High mobility group protein B3Add BLAST200

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3N6-acetyllysineBy similarity1
Disulfide bondi23 ↔ 45In disulfide HMGB3; alternateBy similarity
Modified residuei23Cysteine sulfonic acid (-SO3H); alternateBy similarity1
Modified residuei30N6-acetyllysineBy similarity1
Modified residuei43N6-acetyllysineBy similarity1
Modified residuei45Cysteine sulfonic acid (-SO3H); alternateBy similarity1
Modified residuei98PhosphoserineBy similarity1
Modified residuei104Cysteine sulfonic acid (-SO3H)By similarity1
Modified residuei112N6-acetyllysineBy similarity1
Modified residuei139N6-acetyllysineBy similarity1

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 similarity1 Publication

Keywords - PTMi

Acetylation, Disulfide bond, Oxidation, Phosphoprotein

Proteomic databases

EPDiO15347
MaxQBiO15347
PaxDbiO15347
PeptideAtlasiO15347
PRIDEiO15347
ProteomicsDBi48596
TopDownProteomicsiO15347

PTM databases

iPTMnetiO15347
PhosphoSitePlusiO15347

Expressioni

Tissue specificityi

Expressed predominantly in placenta.

Gene expression databases

BgeeiENSG00000029993 Expressed in 189 organ(s), highest expression level in secondary oocyte
CleanExiHS_HMGB3
ExpressionAtlasiO15347 baseline and differential
GenevisibleiO15347 HS

Organism-specific databases

HPAiHPA062583

Interactioni

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi109392, 31 interactors
IntActiO15347, 11 interactors
STRINGi9606.ENSP00000359393

Structurei

Secondary structure

1200
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO15347
SMRiO15347
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO15347

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi181 – 200Asp/Glu-rich (acidic)Add BLAST20

Sequence similaritiesi

Belongs to the HMGB family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0381 Eukaryota
COG5648 LUCA
GeneTreeiENSGT00760000119164
HOGENOMiHOG000197861
HOVERGENiHBG009000
InParanoidiO15347
KOiK11296
OMAiHTRKPRK
OrthoDBiEOG091G0P81
PhylomeDBiO15347
TreeFamiTF105371

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
IPR031077 HMGB3
PANTHERiPTHR13711:SF144 PTHR13711:SF144, 1 hit
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 (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 3 potential isoforms that are computationally mapped.Show allAlign All

O15347-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAKGDPKKPK GKMSAYAFFV QTCREEHKKK NPEVPVNFAE FSKKCSERWK
60 70 80 90 100
TMSGKEKSKF DEMAKADKVR YDREMKDYGP AKGGKKKKDP NAPKRPPSGF
110 120 130 140 150
FLFCSEFRPK IKSTNPGISI GDVAKKLGEM WNNLNDSEKQ PYITKAAKLK
160 170 180 190 200
EKYEKDVADY KSKGKFDGAK GPAKVARKKV EEEDEEEEEE EEEEEEEEDE
Length:200
Mass (Da):22,980
Last modified:January 23, 2007 - v4
Checksum:i31C090FAA4D581E6
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E7ES08E7ES08_HUMAN
High mobility group protein B3
HMGB3
188Annotation score:
E7EQU1E7EQU1_HUMAN
High mobility group protein B3
HMGB3
193Annotation score:
E9PES6E9PES6_HUMAN
High mobility group protein B3
HMGB3
153Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti13M → T in CAA71143 (PubMed:9370291).Curated1
Sequence conflicti52M → V in CAA71143 (PubMed:9370291).Curated1
Sequence conflicti187E → Q in CAA71143 (PubMed:9370291).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04955851T → A. Corresponds to variant dbSNP:rs16995792Ensembl.1
Natural variantiVAR_06416256E → Q1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10043 mRNA Translation: CAA71143.1
AF003626 Genomic DNA No translation available.
BC070482 mRNA Translation: AAH70482.1
CCDSiCCDS35428.1
RefSeqiNP_001288157.1, NM_001301228.1
NP_001288158.1, NM_001301229.1
NP_001288160.1, NM_001301231.1
NP_005333.2, NM_005342.3
UniGeneiHs.19114

Genome annotation databases

EnsembliENST00000325307; ENSP00000359393; ENSG00000029993
ENST00000448905; ENSP00000442758; ENSG00000029993
GeneIDi3149
KEGGihsa:3149
UCSCiuc004fep.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10043 mRNA Translation: CAA71143.1
AF003626 Genomic DNA No translation available.
BC070482 mRNA Translation: AAH70482.1
CCDSiCCDS35428.1
RefSeqiNP_001288157.1, NM_001301228.1
NP_001288158.1, NM_001301229.1
NP_001288160.1, NM_001301231.1
NP_005333.2, NM_005342.3
UniGeneiHs.19114

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2EQZNMR-A1-79[»]
2YQINMR-A91-164[»]
ProteinModelPortaliO15347
SMRiO15347
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109392, 31 interactors
IntActiO15347, 11 interactors
STRINGi9606.ENSP00000359393

PTM databases

iPTMnetiO15347
PhosphoSitePlusiO15347

Polymorphism and mutation databases

BioMutaiHMGB3

Proteomic databases

EPDiO15347
MaxQBiO15347
PaxDbiO15347
PeptideAtlasiO15347
PRIDEiO15347
ProteomicsDBi48596
TopDownProteomicsiO15347

Protocols and materials databases

DNASUi3149
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000325307; ENSP00000359393; ENSG00000029993
ENST00000448905; ENSP00000442758; ENSG00000029993
GeneIDi3149
KEGGihsa:3149
UCSCiuc004fep.4 human

Organism-specific databases

CTDi3149
DisGeNETi3149
EuPathDBiHostDB:ENSG00000029993.14
GeneCardsiHMGB3
HGNCiHGNC:5004 HMGB3
HPAiHPA062583
MalaCardsiHMGB3
MIMi300193 gene
300915 phenotype
neXtProtiNX_O15347
OpenTargetsiENSG00000029993
PharmGKBiPA35092
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0381 Eukaryota
COG5648 LUCA
GeneTreeiENSGT00760000119164
HOGENOMiHOG000197861
HOVERGENiHBG009000
InParanoidiO15347
KOiK11296
OMAiHTRKPRK
OrthoDBiEOG091G0P81
PhylomeDBiO15347
TreeFamiTF105371

Miscellaneous databases

EvolutionaryTraceiO15347
GeneWikiiHMGB3
GenomeRNAii3149
PROiPR:O15347
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000029993 Expressed in 189 organ(s), highest expression level in secondary oocyte
CleanExiHS_HMGB3
ExpressionAtlasiO15347 baseline and differential
GenevisibleiO15347 HS

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
IPR031077 HMGB3
PANTHERiPTHR13711:SF144 PTHR13711:SF144, 1 hit
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
ProtoNetiSearch...

Entry informationi

Entry nameiHMGB3_HUMAN
AccessioniPrimary (citable) accession number: O15347
Secondary accession number(s): O95556, Q6NS40
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 162 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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