Histone

Histones (H) are the major protein components of chromatin which help to pack the DNA in the nucleosomes. H2A, H2B, H3 and H4 are core histones while H1 and H5 are linker histones^[1]. The nucleosome is the repeated unit of the chromatin consisting of a core which contains 8 histone molecules (two copies of H2A, H2B, H3 and H4) wrapped by ca. 140 base pairs of DNA^[2]. The chromatin is made of nucleosome cores separated by a linker region of upto 80 base pairs of DNA associated with histones H1 and H5.

For the hyperthermophilic histones see Archaeal Histones.
For nucleosome structure see
User:Eric Martz/Nucleosomes
Nucleosome structure
Nucleosomes
Nucleosome structure (Spanish)

3D Structures of histone

Histone 3D structures

Yeast H3 (green), H4 (pink) and anti-silencing protein (grey) complex with sulfate, glycerol and Zn+2 ion (grey), 2hue

Drag the structure with the mouse to rotate

3D Structures of histone3D Structures of histone

Updated on 31-July-2019

Histone
- 1yqa – yH1 (mutant) – yeast – NMR
- 1uss, 1ust, 1uhm – yH1 globular domain - NMR
- 1ghc – cH1 – chicken - NMR
- 2xd7, 1zr3, 1zr5, 2fxk – hH2A macro domain – human
- 4cay – hH2A +H2B
- 1yd9 – H2A macro domain – rat
- 1ku5 – HPHA – Pyrococcus horikoshii
- 1b67, 1b6w, 1a7w, 1hta – MfHMFA – Methanococcus fervidus
- 1bfm – MfHB - NMR
- 1f1e – H – Methanopyrus kandleri
- 1hst – cH5
- 3iid, 3iif – H2A macro domain + ADP-ribose
- 2g9a, 2g99, 2h13 – H3 + WD-repeat protein
- 1pfb – H3 + polycomb protein – Strongylocentrus purpuratus
Nucleosome core
- 6n89, 6n88 – hH1 + importin – Cryo EM
- 6h8p – hH1 + histone-lysine methyltransferase
- 3r45 - hH4 + H3-like centromeric protein + Holliday junction recognition protein
- 3nqj, 3nqu - hH4 + H3-like centromeric protein
- 5vey - hH2A + H2B + polyubiquitin
- 5fug - hH2A + H2B + YL-1
- 4nft - hH2A + H2B + ANP32E
- 6miq, 6mio, 6min – hH3 + TFIID
- 6mim, 6mil – hH3 + AF9
- 5ja4, 5bnv – hH3.3 + H4 + TONSL + MCM2
- 5bo0, 5bnx – hH3.2 + H4 + ASF1B + MCM2
- 6mlc - hH4 + histone-lysine methyltransferase
- 6hbo – hH3.3 + histone-lysine methyltransferase - NMR
- 6o7g - XlH4 + histone-lysine methyltransferase – NMR
- 3qzs, 3qzt – XlH4 + nucleosome-remodeling factor subunit BPTF – Xenopus laevis
- 4h9n, 4h9o, 4h9p, 4h9q, 4h9r, 4h9s, 4hga - XlH3.3 (mutant) + H4 + death domain-associated protein 6
- 5kdm - XlH3.3 + H4 + death domain-associated protein + tegument protein
- 2io5 - XlH3.1 + H4 + anti-silencing protein
- 5g2e - XlH2A + H2B + NAP1
- 6n1z - XlH2A + H2B + importin
- 5bsa, 5bs7 – XlH3.2 + H4 + SPT2
- 4eo5 - XlH3.2 (mutant) + H4 (mutant) + histone chaperone ASF1
- 4ld9 - XlH3.2 + H4 + H2A + H2B + widom sequence reverse + SIR3
- 2l5a - yH4/H3-like centromeric protein/SCM3
- 2jss - yH2A/H2B + CHZ1 – NMR
- 4wnn – yH32A + H2B + SPT2
- 2hue - yH3 + H4 + anti-silencing protein
- 2xql, 3c9k - cH3.2 + H4 + H2A + H2B – EM
- 4uuz – DmH3 + H4 + DNA replication licensing factor – Drosophila melanogaster
- 2yfv, 2yfw - H4 + H3-like centromeric protein + SCM3 – Kluyveromyces lactis
Human nucleosome core + DNA
- 3an2, 4x23 – hH4 + H2A + H2B + H3-like centromeric protein + DNA
- 3av1, 2av2, 3av2, 3waa, 3wa9, 3w99, 3w98, 3w97, 3w96, 5x7x, 3a6n, 3afa, 2cv5, 5jrg, 5gxq, 5gt3, 5gt0, 5gsu, 5gse, 5cpk, 5cpj, 5cpi, 5b33, 5b32, 5b31, 5b2j, 5b2i, 5b24, 5b0z, 5b0y, 5ay8, 5avc, 5avb, 5av9, 5av8, 5av6, 5av5, 5z5t, 4ym6, 4ym5, 5y0c, 5onw, 5ong, 5omx – hH3.2 + H4 + H2A + H2B + DNA
- 5x0y, 5x0x – hH3 + H4 + H2A + H2B + DNA + SNF2
- 5z30 – hH3.1 + H4 + H2A (mutant) + H2B + DNA
- 5y0d – hH3.1 + H4 + H2A + H2B (mutant) + DNA
- 4qlc – hH3 + H4 + H2A + H2B + H5 + DNA
- 6r25 – hH3 + H4 + H2A + H2B + NPAC + lysine-specific histone demethylase + DNA – Cryo EM
- 3ayw, 3aze, 3azf, 3azg, 3azh - hH3.1 (mutant) + H4 + H2A + H2B + DNA
- 6r94, 6r93 - hH3.1 + H4 + H2A + H2B + DNA – Cryo EM
- 6r92, 6r91, 6r90, 6r8z, 6r8y - hH3.1 + H4 + H2A + H2B + DNA damage-binding protein + DNA – Cryo EM
- 3azi, 3azj, 3azk, 3azl, 3azm, 3azn, 5b40 - hH3.1 + H4 (mutant) + H2A + H2B + DNA
- 5e5a - hH3.2 + H4 + H2A + H2B + IE1 + DNA
- 6hkt - hH3 + H2A + H2B + DNA
- 5xf5, 5xf4, 5xf3 - hH3.1 + H4 + H2A + H2B + Ru derivative + DNA
Xenopus nucleosome core + DNA
- 6r1t - XlH3 + H2A + H2B + DNA – Cryo EM
- 3mnn, 3o62, 3lz0, 3lz1, 3lel, 3kuy, 3c1b, 3c1c, 2nzd, 2fj7, 1zbb, 1s32, 1p34, 1p3a, 1p3b, 1p3f, 1p3g, 1p3i, 1p3k, 1p3l, 1p3m, 1p3o, 1p3p, 1m18, 1m19, 1m1a, 1kx3, 1kx4, 1kx5, 1aoi, 3reh, 3rei, 3rej, 3rek, 3rel, 3ut9, 3uta, 3utb, 5f99, 5dnn, 5dnm, 5cp6, 4z66, 4ys3, 4xzq, 5oy7, 5oxv - XlH3.2 + H4 + H2A + H2B + DNA
- 6fq8, 6fq6, 6fq5, 6esi, 6esh, 6esg, 6esf - XlH3.2 + H4 + H2A + H2B + DNA – Cryo EM
- 5nl0 - XlH3.2 + H4 + H2A + H2B + H1.0 + DNA
- 6om3 - XlH3.2 + H4 + H2A + H2B + origin recognition complex + DNA
- 6jm9 - XlH3.2 + H4 + H2A + H2B + histone-lysine methyltransferase + DNA – Cryo EM
- 6o96, 6nqa, 6nog, 6nn6, 6nj9, 6jma, 6j99 - XlH3.2 + H4 + H2A + H2B + histone-lysine methyltransferase + ubiquitin + DNA – Cryo EM
- 6iy3, 6iy2 - XlH3.2 + H4 + H2A + H2B + SNF2H + ADP + DNA – Cryo EM
- 5o9g - XlH3.2 + H4 + H2A + H2B + CHD1 + DNA – Cryo EM
- 6ftx - XlH3.1 + H4 + H2A + H2B + CHD1 + ubiquitin + DNA – Cryo EM
- 6hts - XlH3.1 + H4 + H2A + H2B + RuvB + CHD1 + actin-related protein + DNA – Cryo EM
- 6ne3 - XlH3.2 (mutant) + H4 + H2A (mutant) + H2B + SNF2H + DNA – Cryo EM
- 5mlu - XlH3.2 + H4 + H2A + H2B + PFV GAG peptide + DNA
- 5kgf - XlH3.2 + H4 + H2A + H2B + 53BP1 + ubiquitin + DNA
- 5hq2 - XlH3.2 + H4 + H2A + H2B + SRM1 + SetD8 + DNA
- 4zux - XlH3.2 + H4 + H2A + H2B + Saga-associated factors + polyubiquitin + UBP8 + DNA
- 4xuj - XlH3.2 + H4 + H2A + H2B + Ru derivative + DNA
- 4xu9 - XlH3.2 (mutant) + H4 + H2A + H2B + Pt derivative + DNA
- 4xu8 - XlH3.2 + H4 + H2A + H2B (mutant) + Pt derivative + DNA
- 2f8n - XlH3.1 + H4 + H2A + H2B + H3 + H2A macro domain + DNA
- 1zla – XlH3 + H4 + H2A + H2B + H3 + antigen + DNA
- 3mgp, 3mgq, 3mgr, 3mgs, 3lja, 3b6f, 3b6g, 4j8u, 4j8v, 4j8w, 4j8x, 4kgc, 5xf6 - XlH3.2 + H4 + H2A + H2B + metal ion + DNA
- 3kxb - XlH3.2 (mutant) + H4 + H2A + H2B (mutant) + DNA
- 3kwq - XlH3.2 (mutant) + H4 + H2A + H2B + DNA
- 3mvd - XlH3.2 + H4 + H2A + H2B + regulator of chromosome condensation + DNA
- 3tu4 - XlH3.2 + H4 + H2A + H2B + regulatory protein SIR3 + DNA
- 4r8p - XlH3.2 + H4 + H2A + H2B + polycomb complex protein + ring finger protein + DNA
- 6r1u – XlH3.2 + H4 + H2A + H2B + lysine-specific histone demethylase + DNA – Cryo EM
- 6k1p, 6jyl, 6iro – XlH3 + H4 + H2A + H2B + ISWI + ADP + DNA – Cryo EM
- 6g0l – XlH3 + H4 + H2A + H2B + CHD1 + DNA – Cryo EM
Other nucleosome core + DNA
- 1u35 - mH3.1 + H2A + H2B + His2A macro domain + DNA – mouse
- 5xm1, 5xm0 – mH3 + H4 + H2A + H2B + DNA
- 1f66 - XlH3 + mH4 + hH2A + XlH2B + DNA
- 5b1m, 5b1l - mH3 + H4 + H2A + H2B + DNA
- 2aro, 1tzy, 1hq3, 2hio, 1hio - cH3 + H4 + H2A + H2B
- 1eqz - cH3 + H4 + H2A + H2B + DNA
- 2pyo, 2nqb, 3nqb - DmH3 + H4 + H2A + H2B + DNA
- 5wcu - DmH3 + H4 + H2A + H2B + H5 + DNA
- 4x23 - DmH3 + H4 + H2A + H2B + centromeric protein C + DNA
- 6dzt - DmH3 + H4 + H2A + H2B + antibody + DNA
- 6j51, 6j50, 6j4z, 6j4y, 6j4x, 6j4w, 6inq, 6i84, 6a5u, 6a5t, 6a5r, 6a5p, 6a5o, 6a5l – yH3.3 + H4 + H2A + H2B + RNA polymerase + RNA + DNA – Cryo EM
- 6ir9 – yH3.3 + H4 + H2A + H2B + RNA polymerase + SPT4 + SPT5 + RNA + DNA – Cryo EM
- 6gen, 6gej – yH3 + H4 + H2A + H2B + SWI1 + actin-like protein + vacuolar protein sorting-associated + RNA + DNA – Cryo EM
- 1id3 - yH3 + H4 + H2A + H2B + DNA
- 4jjn, 4kud - yH3 + H4 + H2A.2 + H2B.2 + SIR3 + DNA
- 5zbb, 5zba - yH3 + H4 + RTT109 + ASF1
- 5z3v, 5z3u, 5z3t, 5z3o, 5z3l - yH3.2 + H4 + H2A + H2B + SNF2 + ADP + DNA – Cryo EM

2aro, 1tzy, 1hq3, 2hio, 1hio - cH3 + H4 + H2A + H2B

- 6fml – H3.2 + H4 + H2A + H2B + RuvB + actin-related protein + IES6 + DNA – Chaetomium thermophilum - Cryo EM

ReferencesReferences

↑ Marino-Ramirez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Rev Proteomics. 2005 Oct;2(5):719-29. PMID:16209651 doi:http://dx.doi.org/10.1586/14789450.2.5.719
↑ Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science. 1974 May 24;184(4139):868-71. PMID:4825889

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Michal Harel, Alexander Berchansky, Ann Taylor, Karsten Theis

[1] Marino-Ramirez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Rev Proteomics. 2005 Oct;2(5):719-29. PMID:16209651 doi:http://dx.doi.org/10.1586/14789450.2.5.719

[2] Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science. 1974 May 24;184(4139):868-71. PMID:4825889

[1]

[2]

Histone

3D Structures of histone

3D Structures of histone3D Structures of histone

ReferencesReferences

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