/ H3 / Variant: cenH3

Description

cenH3 is a centromere-specific histone variant, which replaces canonical H3 in centromeric nucleosomes. It is required for kinetochore formation, mitotic progression and chromosome segregation. cenH3 has an extended L1-loop and its N-terminal tail is very different from other H3 variants. cenH3s have an extended L1-loop and usually replace Phe84 in canonical H3 with Trp, and Thr 107 with Ala, Cys, or Ser. cenH3s ususally lack a conserved glutamine in the alpha1 helix of the histone fold. cenH3s typically have only about 50-60% amino acid identity to canonical H3 in the histone fold domain and no conservation of the N-terminus.
Alternate names: CENP-A, cid, CNA1, CNP1, Cse4, HCP-3, HTR12

Features

Below, you can explore the features of cenH3 from Homo sapiens, if available and how it compares to the canonical histones of the same type (first row). Canonical histone is shown in the first row, the names and descriptions of each feature can be found underneath. To explore variants from other species, please browse our curated sequences, automatically extracted sequences, or by taxonomy.

Keys: red - identical residues, blue - different residues (if more than one sequence).
Variant features
Q>X
Site of characteristic Gln substitution (canonical > variant).
ext
L1-loop extension
F>W
Site of characteristic Phe > Tyr substitution (canonical > variant).
T>X
Site of characteristic Thr > Ala, Cys, or Ser substitution (canonical > variant).
General histone type features
alphaN
AlphaN-helix
R1
Minor groove arginine at the alphaN DNA binding site, SHL ±6.5
R2
Minor groove arginine at alpha1-alpha1 DNA binding site, SHL ±1.5
alpha1
Alpha1-helix, first helix of histone fold
loopL1
L1 loop connecting first and second helices of histone fold. Part of the L1L2 DNA binding site formed by H3 and H4 at SHL ±0.5.
beta1
Beta-strand in L1L2 DNA binding site
R3
Minor groove arginine at L1L2 DNA binding site, SHL ±2.5
alpha2
Alpha2-helix, second helix of histone fold
loopL2
L2 loop connecting second and third helices of histone fold. Part of L1L2 DNA binding site formed by H3 and H4 at SHL ±2.5.
beta2
Beta-strand in L1L2 DNA binding site
alpha3
Alpha3-helix, third helix of histone fold

References

  1. Talbert PB, Ahmad K, et al. "A unified phylogeny-based nomenclature for histone variants." Epigenetics Chromatin, 2012. PMID: 22650316
  2. Malik HS and Henikoff S. "Major evolutionary transitions in centromere complexity." Cell, 2009. PMID: 19766562
  3. Steiner FA and Henikoff S. "Diversity in the organization of centromeric chromatin." Curr Opin Genet Dev, 2015. PMID: 25956076
  4. Bui M, Walkiewicz MP, et al. "The CENP-A nucleosome: a battle between Dr Jekyll and Mr Hyde." Nucleus, 2013. PMID: 23324462
  5. Tachiwana H, Kagawa W, et al. "Crystal structure of the human centromeric nucleosome containing CENP-A." Nature, 2011. PMID: 21743476
  6. Malik HS and Henikoff S. "Phylogenomics of the nucleosome." Nat Struct Biol, 2003. PMID: 14583738
A set of manually selected and validated histone sequences is listed in the table. Click on an entry in the table to update the annotated sequence preview: a variant will be compared with the canonical histone from the same species (if available). Alternatively, tick mark the sequences and use toolbar to view MSA, export or add to basket. Use search or filters to find particular entries.
Keys: red - identical residues, blue - different residues (if more than one sequence). For feature legend see summary tab.
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Note: variant classification might be ambigous between very similar variants. Classification scores against all variant models are available via advanced menu.
Features characteristic for a given histone type/variant are marked below the consensus sequence. For feature description see summary tabs of the corresponding variants pages.
Keys: red - 80% identical, blue - 50% identical columns. X-ambigous positions in consensus sequence.