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Protein

High mobility group protein B3

Gene

HMGB3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds preferentially single-stranded DNA and unwinds double-stranded DNA.By similarity

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

  1. chromatin binding Source: GO_Central
  2. DNA binding, bending Source: UniProtKB
  3. double-stranded DNA binding Source: UniProtKB
  4. poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  1. chromatin remodeling Source: GO_Central
  2. DNA recombination Source: UniProtKB
  3. multicellular organismal development Source: ProtInc
  4. negative regulation of B cell differentiation Source: Ensembl
  5. negative regulation of myeloid cell differentiation Source: Ensembl
  6. regulation of transcription, DNA-templated Source: GO_Central
Complete GO annotation...

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:5004. HMGB3.

Subcellular locationi

Nucleus PROSITE-ProRule annotation. Chromosome By similarity

GO - Cellular componenti

  1. chromosome Source: UniProtKB-SubCell
  2. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, 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

MIMi300915. phenotype.
PharmGKBiPA35092.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 200200High mobility group protein B3PRO_0000048539Add
BLAST

Proteomic databases

MaxQBiO15347.
PaxDbiO15347.
PeptideAtlasiO15347.
PRIDEiO15347.

PTM databases

PhosphoSiteiO15347.

Expressioni

Tissue specificityi

Expressed predominantly in placenta.

Gene expression databases

BgeeiO15347.
CleanExiHS_HMGB3.
ExpressionAtlasiO15347. baseline and differential.
GenevestigatoriO15347.

Organism-specific databases

HPAiHPA062583.

Interactioni

Protein-protein interaction databases

BioGridi109392. 21 interactions.
IntActiO15347. 1 interaction.
MINTiMINT-5002211.
STRINGi9606.ENSP00000359393.

Structurei

Secondary structure

1
200
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 83Combined sources
Helixi15 – 3016Combined sources
Helixi38 – 5013Combined sources
Helixi54 – 7825Combined sources
Helixi99 – 11416Combined sources
Helixi120 – 13314Combined sources
Helixi136 – 16025Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EQZNMR-A1-79[»]
2YQINMR-A91-164[»]
ProteinModelPortaliO15347.
SMRiO15347. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO15347.

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

eggNOGiNOG320947.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiO15347.
KOiK11296.
OMAiVIRIRMA.
PhylomeDBiO15347.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
[Graphical view]
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.

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 22, 2007 - v4
Checksum:i31C090FAA4D581E6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti13 – 131M → T in CAA71143 (PubMed:9370291).Curated
Sequence conflicti52 – 521M → V in CAA71143 (PubMed:9370291).Curated
Sequence conflicti187 – 1871E → Q in CAA71143 (PubMed:9370291).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti51 – 511T → A.
Corresponds to variant rs16995792 [ dbSNP | Ensembl ].
VAR_049558
Natural varianti56 – 561E → Q.1 Publication
VAR_064162

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.3. human.

Keywords - Coding sequence diversityi

Polymorphism

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2EQZNMR-A1-79[»]
2YQINMR-A91-164[»]
ProteinModelPortaliO15347.
SMRiO15347. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109392. 21 interactions.
IntActiO15347. 1 interaction.
MINTiMINT-5002211.
STRINGi9606.ENSP00000359393.

PTM databases

PhosphoSiteiO15347.

Proteomic databases

MaxQBiO15347.
PaxDbiO15347.
PeptideAtlasiO15347.
PRIDEiO15347.

Protocols and materials databases

DNASUi3149.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000325307; ENSP00000359393; ENSG00000029993.
ENST00000448905; ENSP00000442758; ENSG00000029993.
GeneIDi3149.
KEGGihsa:3149.
UCSCiuc004fep.3. human.

Organism-specific databases

CTDi3149.
GeneCardsiGC0XP150148.
HGNCiHGNC:5004. HMGB3.
HPAiHPA062583.
MIMi300193. gene.
300915. phenotype.
neXtProtiNX_O15347.
PharmGKBiPA35092.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG320947.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiO15347.
KOiK11296.
OMAiVIRIRMA.
PhylomeDBiO15347.
TreeFamiTF105371.

Miscellaneous databases

EvolutionaryTraceiO15347.
GeneWikiiHMGB3.
GenomeRNAii3149.
NextBioi12480.
PROiO15347.
SOURCEiSearch...

Gene expression databases

BgeeiO15347.
CleanExiHS_HMGB3.
ExpressionAtlasiO15347. baseline and differential.
GenevestigatoriO15347.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
[Graphical view]
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. "Isolation of human and mouse HMG2a cDNAs: evidence for an HMG2a-specific 3' untranslated region."
    Wilke K., Wiemann S., Gaul R., Gong W., Poustka A.
    Gene 198:269-274(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Eye.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "Solution structure of the first and second HMG-box domain from high mobility group protein B3."
    RIKEN structural genomics initiative (RSGI)
    Submitted (MAR-2008) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 1-164.
  6. Cited for: VARIANT GLN-56.
  7. "Identification of an HMGB3 frameshift mutation in a family with an X-linked colobomatous microphthalmia syndrome using whole-genome and X-exome sequencing."
    Scott A.F., Mohr D.W., Kasch L.M., Barton J.A., Pittiglio R., Ingersoll R., Craig B., Marosy B.A., Doheny K.F., Bromley W.C., Roderick T.H., Chassaing N., Calvas P., Prabhu S.S., Jabs E.W.
    JAMA Ophthalmol. 132:1215-1220(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN MCOPS13.

Entry informationi

Entry nameiHMGB3_HUMAN
AccessioniPrimary (citable) accession number: O15347
Secondary accession number(s): O95556, Q6NS40
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 26, 2002
Last sequence update: January 22, 2007
Last modified: March 3, 2015
This is version 129 of the entry and version 4 of the sequence. [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. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.