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P02281

- H2B11_XENLA

UniProt

P02281 - H2B11_XENLA

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Protein

Histone H2B 1.1

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

Core component of nucleosome. 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. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B 1.1
Short name:
H2B1.1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-6493994. hist1h2bj.

Subcellular locationi

GO - Cellular componenti

  1. nucleosome Source: UniProtKB-KW
  2. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 126125Histone H2B 1.1PRO_0000071854Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysineBy similarity
Modified residuei13 – 131N6-acetyllysineBy similarity
Modified residuei15 – 151Phosphoserine1 Publication
Modified residuei16 – 161N6-acetyllysineBy similarity
Modified residuei21 – 211N6-acetyllysineBy similarity
Glycosylationi113 – 1131O-linked (GlcNAc)By similarity
Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

Post-translational modificationi

Monoubiquitination of Lys-121 by BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation.By similarity
Phosphorylated on Ser-15 during developmentally programmed apoptosis; which may facilitate apoptotic chromatin condensation.1 Publication
GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).By similarity

Keywords - PTMi

Acetylation, Glycoprotein, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PRIDEiP02281.

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. The octamer wraps approximately 147 bp of DNA.3 Publications

Protein-protein interaction databases

BioGridi103448. 6 interactions.
DIPiDIP-38577N.
IntActiP02281. 3 interactions.

Structurei

Secondary structure

1
126
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 113
Beta strandi18 – 203
Helixi39 – 4911
Helixi57 – 8428
Beta strandi88 – 903
Helixi92 – 10211
Helixi105 – 12319

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80D/H28-126[»]
1F66X-ray2.60D/H1-126[»]
1KX3X-ray2.00D/H2-126[»]
1KX4X-ray2.60D/H2-126[»]
1KX5X-ray1.94D/H2-126[»]
1M18X-ray2.45D/H2-126[»]
1M19X-ray2.30D/H2-126[»]
1M1AX-ray2.65D/H2-126[»]
1P34X-ray2.70D/H2-126[»]
1P3AX-ray3.00D/H2-126[»]
1P3BX-ray3.00D/H2-126[»]
1P3FX-ray2.90D/H2-126[»]
1P3GX-ray2.70D/H2-126[»]
1P3IX-ray2.30D/H2-126[»]
1P3KX-ray2.90D/H2-126[»]
1P3LX-ray2.40D/H2-126[»]
1P3MX-ray2.90D/H2-126[»]
1P3OX-ray2.75D/H2-126[»]
1P3PX-ray2.70D/H2-126[»]
1S32X-ray2.05D/H5-126[»]
1ZBBX-ray9.00D/H/d/h2-126[»]
1ZLAX-ray2.90D/H2-126[»]
2F8NX-ray2.90H5-126[»]
2FJ7X-ray3.20D/H2-126[»]
2NZDX-ray2.65D/H2-126[»]
3B6FX-ray3.45D/H2-126[»]
3B6GX-ray3.45D/H2-126[»]
3KUYX-ray2.90D/H2-126[»]
3KWQX-ray3.50D/H34-126[»]
3KXBX-ray3.20D/H5-126[»]
3LELX-ray2.95D/H/N/R2-126[»]
3LJAX-ray2.75D/H5-126[»]
3LZ0X-ray2.50D/H2-126[»]
3LZ1X-ray2.50D/H2-126[»]
3MGPX-ray2.44D/H2-126[»]
3MGQX-ray2.65D/H2-126[»]
3MGRX-ray2.30D/H2-126[»]
3MGSX-ray3.15D/H2-126[»]
3MNNX-ray2.50D/H2-126[»]
3MVDX-ray2.90D/H5-126[»]
3O62X-ray3.22D/H5-126[»]
3REHX-ray2.50D/H5-126[»]
3REIX-ray2.65D/H5-126[»]
3REJX-ray2.55D/H5-126[»]
3REKX-ray2.60D/H5-126[»]
3RELX-ray2.70D/H5-126[»]
3TU4X-ray3.00D/H5-126[»]
3UT9X-ray2.20D/H2-126[»]
3UTAX-ray2.07D/H2-126[»]
3UTBX-ray2.20D/H2-126[»]
4J8UX-ray2.38D/H2-126[»]
4J8VX-ray2.58D/H2-126[»]
4J8WX-ray2.41D/H2-126[»]
4J8XX-ray2.87D/H2-126[»]
4KGCX-ray2.69D/H1-126[»]
4KHAX-ray2.35A34-126[»]
4LD9X-ray3.31D/H1-126[»]
ProteinModelPortaliP02281.
SMRiP02281. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02281.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

HOVERGENiHBG007774.
KOiK11252.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P02281-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSAK
Length:126
Mass (Da):13,934
Last modified:January 23, 2007 - v2
Checksum:iDA6C122EC8359FD9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03018 Genomic DNA. Translation: CAA26816.1.
M21287 Genomic DNA. Translation: AAA49768.1.
BC077399 mRNA. Translation: AAH77399.1.
PIRiB92918. HSXLB1.
RefSeqiNP_001086753.1. NM_001093284.1.
UniGeneiXl.46757.

Genome annotation databases

GeneIDi446588.
KEGGixla:446588.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03018 Genomic DNA. Translation: CAA26816.1 .
M21287 Genomic DNA. Translation: AAA49768.1 .
BC077399 mRNA. Translation: AAH77399.1 .
PIRi B92918. HSXLB1.
RefSeqi NP_001086753.1. NM_001093284.1.
UniGenei Xl.46757.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AOI X-ray 2.80 D/H 28-126 [» ]
1F66 X-ray 2.60 D/H 1-126 [» ]
1KX3 X-ray 2.00 D/H 2-126 [» ]
1KX4 X-ray 2.60 D/H 2-126 [» ]
1KX5 X-ray 1.94 D/H 2-126 [» ]
1M18 X-ray 2.45 D/H 2-126 [» ]
1M19 X-ray 2.30 D/H 2-126 [» ]
1M1A X-ray 2.65 D/H 2-126 [» ]
1P34 X-ray 2.70 D/H 2-126 [» ]
1P3A X-ray 3.00 D/H 2-126 [» ]
1P3B X-ray 3.00 D/H 2-126 [» ]
1P3F X-ray 2.90 D/H 2-126 [» ]
1P3G X-ray 2.70 D/H 2-126 [» ]
1P3I X-ray 2.30 D/H 2-126 [» ]
1P3K X-ray 2.90 D/H 2-126 [» ]
1P3L X-ray 2.40 D/H 2-126 [» ]
1P3M X-ray 2.90 D/H 2-126 [» ]
1P3O X-ray 2.75 D/H 2-126 [» ]
1P3P X-ray 2.70 D/H 2-126 [» ]
1S32 X-ray 2.05 D/H 5-126 [» ]
1ZBB X-ray 9.00 D/H/d/h 2-126 [» ]
1ZLA X-ray 2.90 D/H 2-126 [» ]
2F8N X-ray 2.90 H 5-126 [» ]
2FJ7 X-ray 3.20 D/H 2-126 [» ]
2NZD X-ray 2.65 D/H 2-126 [» ]
3B6F X-ray 3.45 D/H 2-126 [» ]
3B6G X-ray 3.45 D/H 2-126 [» ]
3KUY X-ray 2.90 D/H 2-126 [» ]
3KWQ X-ray 3.50 D/H 34-126 [» ]
3KXB X-ray 3.20 D/H 5-126 [» ]
3LEL X-ray 2.95 D/H/N/R 2-126 [» ]
3LJA X-ray 2.75 D/H 5-126 [» ]
3LZ0 X-ray 2.50 D/H 2-126 [» ]
3LZ1 X-ray 2.50 D/H 2-126 [» ]
3MGP X-ray 2.44 D/H 2-126 [» ]
3MGQ X-ray 2.65 D/H 2-126 [» ]
3MGR X-ray 2.30 D/H 2-126 [» ]
3MGS X-ray 3.15 D/H 2-126 [» ]
3MNN X-ray 2.50 D/H 2-126 [» ]
3MVD X-ray 2.90 D/H 5-126 [» ]
3O62 X-ray 3.22 D/H 5-126 [» ]
3REH X-ray 2.50 D/H 5-126 [» ]
3REI X-ray 2.65 D/H 5-126 [» ]
3REJ X-ray 2.55 D/H 5-126 [» ]
3REK X-ray 2.60 D/H 5-126 [» ]
3REL X-ray 2.70 D/H 5-126 [» ]
3TU4 X-ray 3.00 D/H 5-126 [» ]
3UT9 X-ray 2.20 D/H 2-126 [» ]
3UTA X-ray 2.07 D/H 2-126 [» ]
3UTB X-ray 2.20 D/H 2-126 [» ]
4J8U X-ray 2.38 D/H 2-126 [» ]
4J8V X-ray 2.58 D/H 2-126 [» ]
4J8W X-ray 2.41 D/H 2-126 [» ]
4J8X X-ray 2.87 D/H 2-126 [» ]
4KGC X-ray 2.69 D/H 1-126 [» ]
4KHA X-ray 2.35 A 34-126 [» ]
4LD9 X-ray 3.31 D/H 1-126 [» ]
ProteinModelPortali P02281.
SMRi P02281. Positions 5-126.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 103448. 6 interactions.
DIPi DIP-38577N.
IntActi P02281. 3 interactions.

Proteomic databases

PRIDEi P02281.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 446588.
KEGGi xla:446588.

Organism-specific databases

CTDi 8970.
Xenbasei XB-GENE-6493994. hist1h2bj.

Phylogenomic databases

HOVERGENi HBG007774.
KOi K11252.

Miscellaneous databases

EvolutionaryTracei P02281.

Family and domain databases

Gene3Di 1.10.20.10. 1 hit.
InterProi IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000558. Histone_H2B.
[Graphical view ]
PANTHERi PTHR23428. PTHR23428. 1 hit.
Pfami PF00125. Histone. 1 hit.
[Graphical view ]
PRINTSi PR00621. HISTONEH2B.
SMARTi SM00427. H2B. 1 hit.
[Graphical view ]
SUPFAMi SSF47113. SSF47113. 1 hit.
PROSITEi PS00357. HISTONE_H2B. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. Identification of novel conserved upstream sequence elements."
    Perry M., Thomsen G.H., Roeder R.G.
    J. Mol. Biol. 185:479-499(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTER X1H3).
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.
  3. "Histone H2B variants from the erythrocytes of an amphibian, a reptile and a bird."
    van Helden P., Strickland W.N., Brandt W.F., von Holt C.
    Biochim. Biophys. Acta 533:278-281(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-30 AND 63-85.
    Tissue: Erythrocyte.
  4. "Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase."
    Cheung W.L., Ajiro K., Samejima K., Kloc M., Cheung P., Mizzen C.A., Beeser A., Etkin L.D., Chernoff J., Earnshaw W.C., Allis C.D.
    Cell 113:507-517(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-15.
  5. "Crystal structure of the nucleosome core particle at 2.8 A resolution."
    Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J.
    Nature 389:251-260(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
  6. "Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands."
    Suto R.K., Edayathumangalam R.S., White C.L., Melander C., Gottesfeld J.M., Dervan P.B., Luger K.
    J. Mol. Biol. 326:371-380(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
  7. "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions."
    Muthurajan U.M., Bao Y., Forsberg L.J., Edayathumangalam R.S., Dyer P.N., White C.L., Luger K.
    EMBO J. 23:260-271(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.

Entry informationi

Entry nameiH2B11_XENLA
AccessioniPrimary (citable) accession number: P02281
Secondary accession number(s): Q6AZT0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 117 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

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3