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Protein

Histone H1.3

Gene

Hist1h1d

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

Functioni

Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).By similarity1 Publication

GO - Molecular functioni

  • chromatin DNA binding Source: MGI
  • DNA binding Source: MGI
  • poly(A) RNA binding Source: MGI

GO - Biological processi

  • histone H3-K27 trimethylation Source: MGI
  • histone H3-K4 trimethylation Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • nucleosome assembly Source: InterPro
  • nucleosome positioning Source: MGI
  • regulation of transcription from RNA polymerase II promoter Source: MGI
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H1.3
Alternative name(s):
H1 VAR.4
H1d
Gene namesi
Name:Hist1h1d
Synonyms:H1f3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:107502. Hist1h1d.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype. Triple-deficient mice (HIST1H1C/HIST1H1D/HIST1H1E) die by midgestation with a broad range of defects. These embryos have about 50% of the normal ratio of H1 to nucleosomes, demonstrating that critical levels of total H1 histones are essential for mouse embryogenesis.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 221220Histone H1.3PRO_0000195916Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources
Modified residuei2 – 21PhosphoserineBy similarity
Modified residuei17 – 171N6-acetyllysineCombined sources
Modified residuei18 – 181PhosphothreonineCombined sources
Modified residuei55 – 551Citrulline1 Publication
Modified residuei105 – 1051Phosphoserine; by PKCBy similarity

Post-translational modificationi

H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter.By similarity
Citrullination at Arg-55 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance.1 Publication

Keywords - PTMi

Acetylation, Citrullination, Phosphoprotein

Proteomic databases

EPDiP43277.
PaxDbiP43277.
PeptideAtlasiP43277.
PRIDEiP43277.
TopDownProteomicsiP43277.

PTM databases

iPTMnetiP43277.
PhosphoSiteiP43277.

Expressioni

Gene expression databases

BgeeiP43277.
CleanExiMM_HIST1H1D.
ExpressionAtlasiP43277. baseline and differential.

Interactioni

Protein-protein interaction databases

BioGridi200144. 1 interaction.
IntActiP43277. 5 interactions.
MINTiMINT-1867306.
STRINGi10090.ENSMUSP00000044395.

Structurei

3D structure databases

ProteinModelPortaliP43277.
SMRiP43277. Positions 37-110.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini37 – 11074H15PROSITE-ProRule annotationAdd
BLAST

Domaini

The C-terminal domain is required for high-affinity binding to chromatin.By similarity

Sequence similaritiesi

Belongs to the histone H1/H5 family.PROSITE-ProRule annotation
Contains 1 H15 (linker histone H1/H5 globular) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG4012. Eukaryota.
ENOG4112541. LUCA.
HOGENOMiHOG000251627.
HOVERGENiHBG009035.
InParanoidiP43277.
KOiK11275.
OMAiYDGEKNN.
OrthoDBiEOG74TX2T.
TreeFamiTF313664.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR005818. Histone_H1/H5_H15.
IPR005819. Histone_H5.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00538. Linker_histone. 1 hit.
[Graphical view]
PRINTSiPR00624. HISTONEH5.
SMARTiSM00526. H15. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51504. H15. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P43277-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSETAPAAPA APAPVEKTPV KKKAKKTGAA AGKRKASGPP VSELITKAVA
60 70 80 90 100
ASKERSGVSL AALKKALAAA GYDVEKNNSR IKLGLKSLVS KGTLVQTKGT
110 120 130 140 150
GASGSFKLNK KAASGEAKPK AKKAGAAKAK KPAGAAKKPK KATGAATPKK
160 170 180 190 200
TAKKTPKKAK KPAAAAGAKK VSKSPKKVKA AKPKKAAKSP AKAKAPKAKA
210 220
SKPKASKPKA TKAKKAAPRK K
Length:221
Mass (Da):22,100
Last modified:January 23, 2007 - v2
Checksum:i19D888981281E55C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti57 – 571G → C in BAC35711 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38128 Genomic DNA. Translation: CAA86288.1.
U62923 Genomic DNA. Translation: AAB05799.1.
AY158906 Genomic DNA. Translation: AAO06217.1.
AK054269 mRNA. Translation: BAC35711.1.
CCDSiCCDS26346.1.
PIRiB35245.
S49482.
RefSeqiNP_663759.3. NM_145713.4.
UniGeneiMm.247046.

Genome annotation databases

EnsembliENSMUST00000045301; ENSMUSP00000044395; ENSMUSG00000052565.
GeneIDi14957.
KEGGimmu:14957.
UCSCiuc007pub.3. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38128 Genomic DNA. Translation: CAA86288.1.
U62923 Genomic DNA. Translation: AAB05799.1.
AY158906 Genomic DNA. Translation: AAO06217.1.
AK054269 mRNA. Translation: BAC35711.1.
CCDSiCCDS26346.1.
PIRiB35245.
S49482.
RefSeqiNP_663759.3. NM_145713.4.
UniGeneiMm.247046.

3D structure databases

ProteinModelPortaliP43277.
SMRiP43277. Positions 37-110.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200144. 1 interaction.
IntActiP43277. 5 interactions.
MINTiMINT-1867306.
STRINGi10090.ENSMUSP00000044395.

PTM databases

iPTMnetiP43277.
PhosphoSiteiP43277.

Proteomic databases

EPDiP43277.
PaxDbiP43277.
PeptideAtlasiP43277.
PRIDEiP43277.
TopDownProteomicsiP43277.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000045301; ENSMUSP00000044395; ENSMUSG00000052565.
GeneIDi14957.
KEGGimmu:14957.
UCSCiuc007pub.3. mouse.

Organism-specific databases

CTDi3007.
MGIiMGI:107502. Hist1h1d.

Phylogenomic databases

eggNOGiKOG4012. Eukaryota.
ENOG4112541. LUCA.
HOGENOMiHOG000251627.
HOVERGENiHBG009035.
InParanoidiP43277.
KOiK11275.
OMAiYDGEKNN.
OrthoDBiEOG74TX2T.
TreeFamiTF313664.

Miscellaneous databases

PROiP43277.
SOURCEiSearch...

Gene expression databases

BgeeiP43277.
CleanExiMM_HIST1H1D.
ExpressionAtlasiP43277. baseline and differential.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR005818. Histone_H1/H5_H15.
IPR005819. Histone_H5.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00538. Linker_histone. 1 hit.
[Graphical view]
PRINTSiPR00624. HISTONEH5.
SMARTiSM00526. H15. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51504. H15. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation of two murine H1 histone genes and chromosomal mapping of the H1 gene complement."
    Drabent B., Franke K., Bode C., Kosciessa U., Bouterfa H., Hameister H., Doenecke D.
    Mamm. Genome 6:505-511(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: BALB/cJ.
    Tissue: Liver.
  2. "Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over 1Mb."
    Wang Z.-F., Krasikov T., Frey M.R., Wang J., Matera A.G., Marzluff W.F.
    Genome Res. 6:688-701(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: C57BL/6J.
  3. "The human and mouse replication-dependent histone genes."
    Marzluff W.F., Gongidi P., Woods K.R., Jin J., Maltais L.J.
    Genomics 80:487-498(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Ovary.
  5. "In vivo phosphorylation of histone H1 variants during the cell cycle."
    Talasz H., Helliger W., Puschendorf B., Lindner H.
    Biochemistry 35:1761-1767(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.
  6. "H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo."
    Fan Y., Nikitina T., Morin-Kensicki E.M., Zhao J., Magnuson T.R., Woodcock C.L., Skoultchi A.I.
    Mol. Cell. Biol. 23:4559-4572(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE, FUNCTION.
  7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-18, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2 AND LYS-17, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.
  9. Cited for: CITRULLINATION AT ARG-55.

Entry informationi

Entry nameiH13_MOUSE
AccessioniPrimary (citable) accession number: P43277
Secondary accession number(s): Q8C6M4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 135 of the entry and version 2 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.