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Protein

Histone H1.3

Gene

HIST1H1D

Organism
Homo sapiens (Human)
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 similarity

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-211227. Activation of DNA fragmentation factor.
R-HSA-2559584. Formation of Senescence-Associated Heterochromatin Foci (SAHF).

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H1.3
Alternative name(s):
Histone H1c
Histone H1s-2
Gene namesi
Name:HIST1H1D
Synonyms:H1F3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:4717. HIST1H1D.

Subcellular locationi

GO - Cellular componenti

  • nuclear chromatin Source: UniProtKB
  • nuclear euchromatin Source: UniProtKB
  • nucleosome Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA29095.

Polymorphism and mutation databases

BioMutaiHIST1H1D.
DMDMi121925.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 221220Histone H1.3PRO_0000195907Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources
Modified residuei2 – 21PhosphoserineCombined sources
Modified residuei17 – 171N6-acetyllysineBy similarity
Modified residuei18 – 181PhosphothreonineCombined sources
Modified residuei55 – 551CitrullineBy similarity
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.By similarity

Keywords - PTMi

Acetylation, Citrullination, Phosphoprotein

Proteomic databases

EPDiP16402.
MaxQBiP16402.
PaxDbiP16402.
PRIDEiP16402.

PTM databases

iPTMnetiP16402.
PhosphoSiteiP16402.
SwissPalmiP16402.

Expressioni

Gene expression databases

BgeeiP16402.
CleanExiHS_HIST1H1D.
GenevisibleiP16402. HS.

Organism-specific databases

HPAiHPA055907.

Interactioni

Protein-protein interaction databases

BioGridi109262. 41 interactions.
IntActiP16402. 8 interactions.
MINTiMINT-3008589.
STRINGi9606.ENSP00000244534.

Structurei

3D structure databases

ProteinModelPortaliP16402.
SMRiP16402. 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.
GeneTreeiENSGT00670000097781.
HOGENOMiHOG000251627.
HOVERGENiHBG009035.
InParanoidiP16402.
KOiK11275.
OrthoDBiEOG74TX2T.
PhylomeDBiP16402.
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.

P16402-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSETAPLAPT IPAPAEKTPV KKKAKKAGAT AGKRKASGPP VSELITKAVA
60 70 80 90 100
ASKERSGVSL AALKKALAAA GYDVEKNNSR IKLGLKSLVS KGTLVQTKGT
110 120 130 140 150
GASGSFKLNK KAASGEGKPK AKKAGAAKPR KPAGAAKKPK KVAGAATPKK
160 170 180 190 200
SIKKTPKKVK KPATAAGTKK VAKSAKKVKT PQPKKAAKSP AKAKAPKPKA
210 220
AKPKSGKPKV TKAKKAAPKK K
Length:221
Mass (Da):22,350
Last modified:January 23, 2007 - v2
Checksum:iDB987FE8DE034D12
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti75 – 751E → K.
Corresponds to variant rs2050949 [ dbSNP | Ensembl ].
VAR_049306

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60747 Genomic DNA. Translation: AAA63186.1.
AF531303 Genomic DNA. Translation: AAN06703.1.
AK312845 mRNA. Translation: BAG35698.1.
AL031777 Genomic DNA. Translation: CAB39189.1.
CH471087 Genomic DNA. Translation: EAW55548.1.
BC104874 mRNA. Translation: AAI04875.1.
BC111971 mRNA. Translation: AAI11972.1.
CCDSiCCDS4597.1.
PIRiB40335.
RefSeqiNP_005311.1. NM_005320.2.
UniGeneiHs.136857.

Genome annotation databases

EnsembliENST00000244534; ENSP00000244534; ENSG00000124575.
GeneIDi3007.
KEGGihsa:3007.
UCSCiuc003nhd.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60747 Genomic DNA. Translation: AAA63186.1.
AF531303 Genomic DNA. Translation: AAN06703.1.
AK312845 mRNA. Translation: BAG35698.1.
AL031777 Genomic DNA. Translation: CAB39189.1.
CH471087 Genomic DNA. Translation: EAW55548.1.
BC104874 mRNA. Translation: AAI04875.1.
BC111971 mRNA. Translation: AAI11972.1.
CCDSiCCDS4597.1.
PIRiB40335.
RefSeqiNP_005311.1. NM_005320.2.
UniGeneiHs.136857.

3D structure databases

ProteinModelPortaliP16402.
SMRiP16402. Positions 37-110.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109262. 41 interactions.
IntActiP16402. 8 interactions.
MINTiMINT-3008589.
STRINGi9606.ENSP00000244534.

PTM databases

iPTMnetiP16402.
PhosphoSiteiP16402.
SwissPalmiP16402.

Polymorphism and mutation databases

BioMutaiHIST1H1D.
DMDMi121925.

Proteomic databases

EPDiP16402.
MaxQBiP16402.
PaxDbiP16402.
PRIDEiP16402.

Protocols and materials databases

DNASUi3007.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000244534; ENSP00000244534; ENSG00000124575.
GeneIDi3007.
KEGGihsa:3007.
UCSCiuc003nhd.4. human.

Organism-specific databases

CTDi3007.
GeneCardsiHIST1H1D.
HGNCiHGNC:4717. HIST1H1D.
HPAiHPA055907.
MIMi142210. gene.
neXtProtiNX_P16402.
PharmGKBiPA29095.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4012. Eukaryota.
ENOG4112541. LUCA.
GeneTreeiENSGT00670000097781.
HOGENOMiHOG000251627.
HOVERGENiHBG009035.
InParanoidiP16402.
KOiK11275.
OrthoDBiEOG74TX2T.
PhylomeDBiP16402.
TreeFamiTF313664.

Enzyme and pathway databases

ReactomeiR-HSA-211227. Activation of DNA fragmentation factor.
R-HSA-2559584. Formation of Senescence-Associated Heterochromatin Foci (SAHF).

Miscellaneous databases

ChiTaRSiHIST1H1D. human.
GeneWikiiHIST1H1D.
GenomeRNAii3007.
NextBioi11924.
PROiP16402.
SOURCEiSearch...

Gene expression databases

BgeeiP16402.
CleanExiHS_HIST1H1D.
GenevisibleiP16402. HS.

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 and characterization of two human H1 histone genes within clusters of core histone genes."
    Albig W., Kardalinou E., Drabent B., Zimmer A., Doenecke D.
    Genomics 10:940-948(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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].
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Thymus.
  4. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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].
    Tissue: Cerebellum.
  7. "Human spleen histone H1. Isolation and amino acid sequences of three minor variants, H1a, H1c, and H1d."
    Ohe Y., Hayashi H., Iwai K.
    J. Biochem. 106:844-857(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-221.
    Tissue: Spleen.
  8. "A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences."
    Parseghian M.H., Henschen A.H., Krieglstein K.G., Hamkalo B.A.
    Protein Sci. 3:575-587(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  9. "The distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin: distribution in human fetal fibroblasts."
    Parseghian M.H., Newcomb R.L., Winokur S.T., Hamkalo B.A.
    Chromosome Res. 8:405-424(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  10. "Distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin II: distribution in human adult fibroblasts."
    Parseghian M.H., Newcomb R.L., Hamkalo B.A.
    J. Cell. Biochem. 83:643-659(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  11. "H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain."
    Th'ng J.P., Sung R., Ye M., Hendzel M.J.
    J. Biol. Chem. 280:27809-27814(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  12. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-18, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  13. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2 AND THR-18, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiH13_HUMAN
AccessioniPrimary (citable) accession number: P16402
Secondary accession number(s): B2R751, Q2M2I2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 151 of the entry and version 2 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

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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. 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.