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Protein

Histone H2A-Bbd type 1

Gene

H2AFB1

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

Functioni

Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with active transcription and mRNA processing. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. Nucleosomes containing this histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome components and are required for mRNA splicing. May participate in spermatogenesis.7 Publications

GO - Molecular functioni

GO - Biological processi

  • chromatin silencing Source: GO_Central
  • mRNA processing Source: UniProtKB
  • nucleosome assembly Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-212300. PRC2 methylates histones and DNA.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-3214858. RMTs methylate histone arginines.
R-HSA-427359. SIRT1 negatively regulates rRNA Expression.
R-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-5250924. B-WICH complex positively regulates rRNA expression.
R-HSA-5334118. DNA methylation.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-HSA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-HSA-73728. RNA Polymerase I Promoter Opening.
R-HSA-73777. RNA Polymerase I Chain Elongation.
R-HSA-912446. Meiotic recombination.
R-HSA-977225. Amyloid fiber formation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A-Bbd type 1
Alternative name(s):
H2A Barr body-deficient
Short name:
H2A.Bbd
Gene namesi
Name:H2AFB1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:22516. H2AFB1.

Subcellular locationi

GO - Cellular componenti

  • nuclear nucleosome Source: UniProtKB
  • nucleus Source: UniProtKB
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134862083.

Polymorphism and mutation databases

BioMutaiH2AFB1.
DMDMi161784332.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 115115Histone H2A-Bbd type 1PRO_0000312805Add
BLAST

Proteomic databases

PaxDbiP0C5Y9.
PeptideAtlasiP0C5Y9.
PRIDEiP0C5Y9.

Expressioni

Tissue specificityi

Present in mature sperm.1 Publication

Gene expression databases

BgeeiP0C5Y9.
CleanExiHS_H2AFB1.
GenevisibleiP0C5Y9. HS.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. May be incorporated into a proportion of nucleosomes, replacing one or more H2A molecules.

Protein-protein interaction databases

BioGridi138883. 2 interactions.
STRINGi9606.ENSP00000346450.

Structurei

3D structure databases

ProteinModelPortaliP0C5Y9.
SMRiP0C5Y9. Positions 21-109.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 11529Docking domainAdd
BLAST

Domaini

The docking domain is responsible for the weaker heterodimerization with H2B.1 Publication

Sequence similaritiesi

Belongs to the histone H2A family.Curated

Phylogenomic databases

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
GeneTreeiENSGT00840000129729.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiP0C5Y9.
KOiK11251.
OMAiRVAPAHH.
OrthoDBiEOG7Z0JZT.
PhylomeDBiP0C5Y9.
TreeFamiTF300137.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.

Sequencei

Sequence statusi: Complete.

P0C5Y9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPRRRRRRGS SGAGGRGRTC SRTVRAELSF SVSQVERSLR EGHYAQRLSR
60 70 80 90 100
TAPVYLAAVI EYLTAKVPEL AGNEAQNSGE RNITPLLLDM VVHNDRLLST
110
LFNTTTISQV APGED
Length:115
Mass (Da):12,697
Last modified:December 4, 2007 - v1
Checksum:i57CA60C8C2F5744B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti109 – 1091Q → K in AAI28035 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86012 Genomic DNA. Translation: CAA59998.1.
CR542230 mRNA. Translation: CAG47026.1.
BX842559 Genomic DNA. Translation: CAI41667.1.
BC128034 mRNA. Translation: AAI28035.1.
CCDSiCCDS35458.1.
PIRiI37901.
RefSeqiNP_001017990.1. NM_001017990.1.
UniGeneiHs.534498.
Hs.592246.
Hs.632841.

Genome annotation databases

EnsembliENST00000620016; ENSP00000484261; ENSG00000274183.
GeneIDi474382.
KEGGihsa:474382.
UCSCiuc004fmu.5. human.

Cross-referencesi

Web resourcesi

Wikipedia

Histone H2A entry

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86012 Genomic DNA. Translation: CAA59998.1.
CR542230 mRNA. Translation: CAG47026.1.
BX842559 Genomic DNA. Translation: CAI41667.1.
BC128034 mRNA. Translation: AAI28035.1.
CCDSiCCDS35458.1.
PIRiI37901.
RefSeqiNP_001017990.1. NM_001017990.1.
UniGeneiHs.534498.
Hs.592246.
Hs.632841.

3D structure databases

ProteinModelPortaliP0C5Y9.
SMRiP0C5Y9. Positions 21-109.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi138883. 2 interactions.
STRINGi9606.ENSP00000346450.

Polymorphism and mutation databases

BioMutaiH2AFB1.
DMDMi161784332.

Proteomic databases

PaxDbiP0C5Y9.
PeptideAtlasiP0C5Y9.
PRIDEiP0C5Y9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000620016; ENSP00000484261; ENSG00000274183.
GeneIDi474382.
KEGGihsa:474382.
UCSCiuc004fmu.5. human.

Organism-specific databases

CTDi474382.
GeneCardsiH2AFB1.
HGNCiHGNC:22516. H2AFB1.
MIMi300445. gene.
neXtProtiNX_P0C5Y9.
PharmGKBiPA134862083.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
GeneTreeiENSGT00840000129729.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiP0C5Y9.
KOiK11251.
OMAiRVAPAHH.
OrthoDBiEOG7Z0JZT.
PhylomeDBiP0C5Y9.
TreeFamiTF300137.

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-212300. PRC2 methylates histones and DNA.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-3214858. RMTs methylate histone arginines.
R-HSA-427359. SIRT1 negatively regulates rRNA Expression.
R-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-5250924. B-WICH complex positively regulates rRNA expression.
R-HSA-5334118. DNA methylation.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-HSA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-HSA-73728. RNA Polymerase I Promoter Opening.
R-HSA-73777. RNA Polymerase I Chain Elongation.
R-HSA-912446. Meiotic recombination.
R-HSA-977225. Amyloid fiber formation.

Miscellaneous databases

GeneWikiiH2AFB1.
GenomeRNAii474382.
PROiP0C5Y9.
SOURCEiSearch...

Gene expression databases

BgeeiP0C5Y9.
CleanExiHS_H2AFB1.
GenevisibleiP0C5Y9. HS.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Investigation of the factor VIII intron 22 repeated region (int22h) and the associated inversion junctions."
    Naylor J.A., Buck D., Green P.M., Williamson H., Bentley D., Giannelli F.
    Hum. Mol. Genet. 4:1217-1224(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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].
  5. "Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA."
    Bao Y., Konesky K., Park Y.-J., Rosu S., Dyer P.N., Rangasamy D., Tremethick D.J., Laybourn P.J., Luger K.
    EMBO J. 23:3314-3324(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN.
  6. "Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I."
    Okuwaki M., Kato K., Shimahara H., Tate S., Nagata K.
    Mol. Cell. Biol. 25:10639-10651(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome."
    Doyen C.M., Montel F., Gautier T., Menoni H., Claudet C., Delacour-Larose M., Angelov D., Hamiche A., Bednar J., Faivre-Moskalenko C., Bouvet P., Dimitrov S.
    EMBO J. 25:4234-4244(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "ATP-dependent chromatin remodeling is required for base excision repair in conventional but not in variant H2A.Bbd nucleosomes."
    Menoni H., Gasparutto D., Hamiche A., Cadet J., Dimitrov S., Bouvet P., Angelov D.
    Mol. Cell. Biol. 27:5949-5956(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way."
    Eirin-Lopez J.M., Ishibashi T., Ausio J.
    FASEB J. 22:316-326(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd."
    Gonzalez-Romero R., Mendez J., Ausio J., Eirin-Lopez J.M.
    Gene 413:1-7(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis."
    Ishibashi T., Li A., Eirin-Lopez J.M., Zhao M., Missiaen K., Abbott D.W., Meistrich M., Hendzel M.J., Ausio J.
    Nucleic Acids Res. 38:1780-1789(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  12. "Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells."
    Tolstorukov M.Y., Goldman J.A., Gilbert C., Ogryzko V., Kingston R.E., Park P.J.
    Mol. Cell 47:596-607(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiH2AB1_HUMAN
AccessioniPrimary (citable) accession number: P0C5Y9
Secondary accession number(s): A0PK90
, P98176, Q5TZB2, Q6FG78, Q96PR7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: December 4, 2007
Last modified: July 6, 2016
This is version 82 of the entry and version 1 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

Miscellaneous

In contrast to other H2A histones, it does not contain the conserved residues that are the target of post-translational modifications.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. 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.