Histone 3D structures

3D Structures of histone3D Structures of histone

Updated on 21-May-2023

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• Histones
  • 2xd7, 1zr3, 2fxk, 1zr5 – hH2A macro domain – human
    
  • 6hq1 – hH1.0 - NMR
    
  • 4cay – hH2A +H2B
    
  • 1yd9 – H2A macro domain – rat
    
  • 1ghc – cH1 – chicken – NMR
    
  • 1hst – cH5
    
  • 2xql, 3c9k - cH3.2 + H4 + H2A + H2B – Cryo EM
    
  • 6k01, 6w4l - XlH2A/H2B - Xenopus laevis
    
  • 7pj1 – DmH2A + H2B – Drosophila melanogaster - NMR
    
  • 6k03 - CeH2A + H2B – Caenorhabditis elegans
    
  • 1yqa – yH1 (mutant) – yeast – NMR
    
  • 1uss, 1ust, 1uhm – yH1 globular domain – NMR
    
  • 1ku5 – HPHA – Pyrococcus horikoshii
    
  • 1b67, 1b6w, 1a7w, 1hta – MfHMFA – Methanococcus fervidus
    
  • 1bfm – MfHB - NMR
    
  • 1f1e – H – Methanopyrus kandleri
    
• Histones complex with protein
  • 6n89, 6n88 – hH1.0 + 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
    
  • 6kbb - hH2A + H2B + SWR-complex protein
    
  • 6miq, 6mio, 6min – hH3 + TFIID
    
  • 6mim, 6mil – hH3 + AF9
    
  • 7v6q – hH3.1 + H4 + NASP + ASF1A
    
  • 7vcl – hH2A + H2B + BKRF4
    
  • 8i17 – hH2A + H2B + SPT16
    
  • 7qxb, 7trf – hH2A + H2B + telomerase reverse transcriptase + RNA – Cryo EM
    
  • 7qxa – hH2A + H2B + telomerase reverse transcriptase + adrenocortical dysplasia protein + RNA – Cryo EM
    
  • 8h0v, 8h0w – hH2A + H2B + H4 + H1.2 in RNA polymerase complex – Cryo EM
    
  • 5ja4, 5bnv – hH3.3 + H4 + TONSL + MCM2
    
  • 7cj0 – hH3.3 + H4 + HDJC9 + MCM2
    
  • 5bo0, 5bnx – hH3.2 + H4 + ASF1B + MCM2
    
  • 7vcq – hH3.3 + H4 + ASF1B + BKRF4
    
  • 6mlc - hH4 + histone-lysine methyltransferase
    
  • 6qxz – hH3.3 + histone-lysine methyltransferase - NMR
    
  • 6vil – hH3.1 + BAHCC1
    
  • 7ciz – hH3.3 + H4 + MCM2
    
  • 3iid, 3iif – hH2A macro domain + ADP-ribose
    
  • 3qzs, 3qzt– XlH4 + nucleosome-remodeling factor subunit BPTF
    
  • 6o7g - XlH4 + histone-lysine methyltransferase – NMR
    
  • 4h9n, 4h9o, 4h9p, 4h9q, 4h9r, 4h9s, 4hga - XlH3.3 (mutant) + H4 + death domain-associated protein
    
  • 5kdm - XlH3.3 + H4 + death domain-associated protein + tegument protein
    
  • 2io5 - XlH3.1 + H4 + anti-silencing protein
    
  • 5g2e, 6k00 - XlH2A + H2B + NAP1
    
  • 6n1z - XlH2A + H2B + importin
    
  • 5bsa, 5bs7 – XlH3.2 + H4 + SPT2
    
  • 6o22 - XlH3.2 + H4 + RTT109 + ASF1
    
  • 7unk - XlH3 + H4 + importin-4 + ASF1
    
  • 4eo5 - XlH3.2 (mutant) + H4 (mutant) + ASF1
    
  • 4ld9 - XlH3.2 + H4 + H2A + H2B + widom sequence reverse + SIR3
    
  • 6k09, 6k0c - CeH2A + H2B + NAP1
    
  • 6m2m – AtH2A + H2B + OSCHZ1 – Arabidopsis thaliana
    
  • 7c7x – AtH2A + H2B + NAP1
    
  • 2l5a - yH4/H3-like centromeric protein/SCM3
    
  • 2jss - yH2A/H2B + CHZ1 – NMR
    
  • 4wnn – yH32A + H2B + SPT2
    
  • 2hue - yH3 + H4 + anti-silencing protein
    
  • 7xay - yH3 + H4 + cytochrome b562 + ASF1
    
  • 4uuz – DmH3 + H4 + DNA replication licensing factor
    
  • 2yfv, 2yfw - KlH4 + H3-like centromeric protein + SCM3 – Kluyveromyces lactis
    
  • 6uph - Kl H3-like centromeric protein + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 1pfb – H3 + polycomb protein – Strongylocentrus purpuratus
    
• Human nucleosome core + 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, 6hkt, 6jou, 6jr0, 6jr1, 6k1i, 6k1j, 6j1k, 6ke9, 6l9h, 6le9, 6ipu, 6iq4, 6jxd, 6kvd, 6ler, 6m3v, 6m44, 6v2k – hH3.1 + H4 + H2A + H2B in nucleosome
    
  • 6r0c, 6t79, 6r94, 6r93, 6l4a, 6t93, 7nl0 – hH3 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 6l49, 6l9z, 6m4d, 6m4g, 6m4h, 6r25, 7u51, 7u52, 7u53, 7v90, 7v9c, 7v9j, 7v9k, 7v9s, 7va4, 7v96, 7xd1, 7xzy, 7y00, 8aag - hH3.1 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 5z30 – hH3.1 + H4 + H2A (mutant) + H2B in nucleosome
    
  • 5y0d – hH3.1 + H4 + H2A + H2B (mutant) in nucleosome
    
  • 4qlc – hH3 + H4 + H2A + H2B + H5 in nucleosome
    
  • 3ayw, 3aze, 3azf, 3azg, 3azh, 5b40 - hH3 (mutant) + H4 + H2A + H2B in nucleosome
    
  • 3azi, 3azj, 3azk, 3azl, 3azm, 3azn - hH3.1 + H4 (mutant) + H2A + H2B in nucleosome
    
  • 7lya - hH3.1 + H4 + H2B in nucleosome – Cryo EM
    
  • 6pwx - hH3.2 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 7pet, 7peu, 7pev, 7pew, 7pex, 7pey, 7pez, 7pf0, 7pf2, 7pf3, 7pf4, 7pf5, 7pf6, 7pfa, 7pfc, 7pfd, 7pfe, 7pff, 7pft, 7pfu, 7pfv, 7pfw, 7pfx - hH3.2 + H4 + H2A + H2B + H1.4 in nucleosome – Cryo EM
    
  • 7x57, 7x58 - hH3.1 + H4 in nucleosome – Cryo EM
    
  • 5xf5, 5xf4, 5xf3 - hH3.1 + H4 + H2A + H2B in nucleosome + Ru derivative
    
• Human nucleosome core + DNA complex with protein
  • 5x0y, 5x0x – hH3 + H4 + H2A + H2B in nucleosome + SNF2
    
  • 3an2, 4x23 – hH4 + H2A + H2B in nucleosome + H3-like centromeric protein
    
  • 6r25 – hH3 + H4 + H2A + H2B in nucleosome + NPAC + lysine-specific histone demethylase – Cryo EM
    
  • 6r92, 6r91, 6r90, 6r8z, 6r8y - hH3.1 + H4 + H2A + H2B in nucleosome + DNA damage-binding protein – Cryo EM
    
  • 5e5a - hH3.2 + H4 + H2A + H2B in nucleosome + IE1
    
  • 7lyb - hH3.1 + H4 + H2B in nucleosome + BRCA1 + BARD1 +UbCH5C – Cryo EM
    
  • 7jzv - hH3.2 (mutant) + H4 + H2A + H2B in nucleosome + BRAC1 – Cryo EM
    
  • 6uxw - hH3.3 + H4 + H2A + H2B in nucleosome + SWI/SNF complex – Cryo EM
    
  • 7ea8 - hH3.3 + H4 + H2A + H2B in nucleosome + SETD2 – Cryo EM
    
  • 7d1z - hH3.1 + H4 + H2A + H2B in nucleosome + SET8 – Cryo EM
    
  • 6muo, 6mup, 7bxt, 7by0 - hH4 + H2A + H2B in nucleosome + CenP-A + CenP-C + CenP-N – Cryo EM
    
  • 6x59, 6x5a, 6xjd, 6y5d, 6y5e, 7jo9, 7joa - hH3.3 + H4 + H2A + H2B in nucleosome + cGAS – Cryo EM
    
  • 7c0m, 7ccq, 7ccr - hH3.1 + H4 + H2A + H2B in nucleosome + cGAS – Cryo EM
    
  • 7bwd - hH3.1 + H4 + H2A + H2B in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 7lyc - hH3.1 + H4 + H2A + H2B in nucleosome + BARD1 + ubiquitin – Cryo EM
    
  • 6usj - hH3.1 + H4 + H2A + H2B in nucleosome + PARP2 – Cryo EM
    
  • 6t7a, 6t7b, 6t7c, 6t7d - hH3.2 + H4 + H2A + H2B in nucleosome + SOX – Cryo EM
    
  • 6t90, 6yov - hH3.2 + H4 + H2A + H2B in nucleosome + SOX + OCT4 – Cryo EM
    
  • 6rny - hH3.3 + H4 + H2A + H2B in nucleosome + integrase – Cryo EM
    
  • 6upk, 6upl - hH3.1 + H4 + H2A + H2B in nucleosome + FACT complex – Cryo EM
    
  • 6v92 – hH3.1 + H4 + H2A + H2B in nucleosome + RSC complex – Cryo EM
    
  • 6fml – hH3.2 + H4 + H2A + H2B in nucleosome + RuvB + actin-related protein + IES6 - Cryo EM
    
• Xenopus nucleosome core + DNA
  • 6r1t, 6px1 - XlH3 + H2A + H2B in nucleosome – 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 in nucleosome
    
  • 6wz5, 6wz9, 7ohc - XlH3.2 + H4 + H2A + H2B in nucleosome - Cryo EM
    
  • 7ktq - XlH3 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 6esi, 6esh, 6esg, 6esf, 6fq8, 6fq6, 6fq5, 6nn6, 6nog, 6nzo, 6px3, 6r1u, 6ugm - XlH3.2 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 4xuj - XlH3.2 + H4 + H2A + H2B in nucleosome + Ru derivative
    
  • 4xu9 - XlH3.2 (mutant) + H4 + H2A + H2B in nucleosome + Pt derivative
    
  • 4xu8 - XlH3.2 + H4 + H2A + H2B (mutant) in nucleosome + Pt derivative
    
  • 2f8n - XlH3.1 + H4 + H2A + H2B + H3 + H2A macro domain in nucleosome
    
  • 1zla – XlH3 + H4 + H2A + H2B + H3 in nucleosome + antigen
  • 3mgp, 3mgq, 3mgr, 3mgs, 3lja 3b6f, 3b6g, 4j8u, 4j8v, 4j8w, 4j8x, 4kgc, 5xf6 - XlH3.2 + H4 + H2A + H2B in nucleosome + metal
    
  • 3kxb - XlH3.2 (mutant) + H4 + H2A + H2B (mutant) in nucleosome
    
  • 3kwq - XlH3.2 (mutant) + H4 + H2A + H2B in nucleosome
    
• Xenopus nucleosome core + DNA complex with protein
  • 6pwx - XlH3.2 + H4 + H2A + H2B in nucleosome + RBBP5 - Cryo EM
    
  • 6pww - XlH3.2 + H4 + H2A + H2B in nucleosome + RBBP5 + WDR5 - Cryo EM
    
  • 6om3 - XlH3.2 + H4 + H2A + H2B in nucleosome + origin recognition complex
    
  • 6vyp - XlH3 (mutant) + H4 + H2A (mutant) + H2B (mutant) in nucleosome + LSD1 + COREST
    
  • 6ryr, 6ryu - XlH3.2 + H4 + H2A + H2B in nucleosome + CHD4 – Cryo EM
    
  • 7crp, 7crr - XlH3 + H4 + H2A + H2B in nucleosome + NSD3 – Cryo EM
    
  • 7crq - XlH3.2 + H4 + H2A + H2B in nucleosome + NSD3 – Cryo EM
    
  • 7at8 - XlH3 + H4 + H2A + H2B in nucleosome + EZH2 + SUZ12 – Cryo EM
    
  • 6vz4 - XlH3 + H4 + H2A + H2B in nucleosome + STH1 + ARP7 + ARP9 + RTT – Cryo EM
    
  • 6kiu, 6kiv, 6kiw, 6kix, 6kiz, 6pwv, 6w5i, 6w5m, 6w5n - XlH3.2 + H4 + H2A + H2B in nucleosome + MLL1 core complex – Cryo EM
    
  • 7ohb - XlH3.2 + H4 + H2A + H2B in nucleosome + TBP – Cryo EM
    
  • 7oh9 - XlH3.2 + H4 + H2A + H2B in nucleosome + TBP + TFIIA – Cryo EM
    
  • 7ea5 - XlH3 (mutant) + H4 + H2A + H2B in nucleosome + SET2 – Cryo EM
    
  • 6s01 - XlH3.2 + H4 + H2A + H2B in nucleosome + PC4 and SFRS1-interacting protein – Cryo EM
    
  • 6iy3, 6iy2 - XlH3.2 + H4 + H2A + H2B in nucleosome + SNF2H – Cryo EM
    
  • 5o9g - XlH3.2 + H4 + H2A + H2B in nucleosome + CHD1 – Cryo EM
    
  • 6x0n - XlH3.2 + H4 + H2A + H2B in nucleosome + PARP2 + HPF1 – Cryo EM
    
  • 7nkx – XlH3 + H4 + H2A + H2B in nucleosome + CHD1 + RNA polymerase – Cryo EM
    
  • 7nky – XlH3 + H4 + H2A + H2B in nucleosome + SPT + FACT + RNA polymerase – Cryo EM
    
  • 6jm9 - XlH3.2 + H4 + H2A + H2B in nucleosome + DOT1 – Cryo EM
    
  • 6jma - XlH3.2 + H4 + H2A + H2B in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 7k6p - XlH3.2 (mutant) + H4 + H2A + H2B (mutant) in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 6nj9 - XlH3.2 (mutant) + H4 + H2A (mutant) + H2B in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 6j99 - XlH3.2 + H4 + H2A + H2B (mutant) in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 6nqa - XlH3.2 + H4 + H2A (mutant) + H2B (mutant) in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 6o96 - XlH3.2 (mutant) + H4 + H2A (mutant) + H2B (mutant) in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 7k6q - XlH3.2 (mutant) + H4 (mutant) + H2A (mutant) + H2B (mutant) in nucleosome + DOT1 + ubiquitin – Cryo EM
    
  • 6ftx - XlH3.1 + H4 + H2A + H2B in nucleosome + CHD1 + ubiquitin – Cryo EM
    
  • 6hts - XlH3.1 + H4 + H2A + H2B in nucleosome + RuvB + CHD1 + actin-related protein – Cryo EM
    
  • 6ne3 - XlH3.2 (mutant) + H4 + H2A (mutant) + H2B in nucleosome + SNF2H – Cryo EM
    
  • 5mlu - XlH3.2 + H4 + H2A + H2B in nucleosome + PFV GAG peptide
    
  • 5kgf - XlH3.2 + H4 + H2A + H2B in nucleosome + 53BP1 + ubiquitin
    
  • 5hq2 - XlH3.2 + H4 + H2A + H2B in nucleosome + SRM1 + SetD8
    
  • 6ven - XlH3.2 (mutant) + H4 + H2A (mutant) + H2B (mutant) in nucleosome + COMPASS + ubiquitin – Cryo EM
    
  • 6uh5 - XlH3.2 + H4 + H2A + H2B (mutant) in nucleosome + COMPASS + ubiquitin – Cryo EM
    
  • 6z6p - XlH3.2 + H3 + H4 + H2A + H2B in nucleosome + HDA1 – Cryo EM
    
  • 6pa7 - XlH3.2 + H4 + H2A + H2B in nucleosome + DNMT3 – Cryo EM
    
  • 6wkr - XlH3.2 + H3 + H4 + H2A + H2B in nucleosome + PRC2 + JARID2 – Cryo EM
    
  • 6lth - XlH3.2 + H3 + H4 + H2A + H2B in nucleosome + BAF complex – Cryo EM
    
  • 6zhx, 6zhy, 7enn - XlH3.2 + H3 + H4 + H2A + H2B in nucleosome + ALC1 – Cryo EM
    
  • 6tem - XlH4 + H2A + H2B in nucleosome + CenP-A – Cryo EM
    
  • 4zux – XlH3.2 + H4 + H2A + H2B in nucleosome + Saga-associated factors + polyubiquitin + UBP8
    
  • 3mvd - XlH3.2 + H4 + H2A + H2B in nucleosome + regulator of chromosome condensation
    
  • 3tu4 - XlH3.2 + H4 + H2A + H2B in nucleosome + regulatory protein SIR3
    
  • 4r8p - XlH3.2 + H4 + H2A + H2B in nucleosome + polycomb complex protein + ring finger protein
    
  • 6k1p, 6jyl, 6iro – XlH3 + H4 + H2A + H2B in nucleosome + ISWI – Cryo EM
    
  • 6kw3, 6kw4, 6kw5, 6tda – XlH3 + H4 + H2A + H2B in nucleosome + RSC complex – Cryo EM
    
  • 6rny - hH3.3 + H4 + H2A + H2B in nucleosome + integrase – Cryo EM
    
  • 6t9l – XlH3 + H4 + H2A + H2B in nucleosome + SAGA complex – Cryo EM
    
• Other nucleosome core + DNA
  • 1u35 - mH3.1 + H2A + H2B + His2A macro domain in nucleosome – mouse
    
  • 5xm1, 5xm0 – mH3 + H4 + H2A + H2B in nucleosome
    
  • 1f66 - XlH3 + mH4 + hH2A + XlH2B in nucleosome
    
  • 5b1m, 5b1l - mH3 + H4 + H2A + H2B in nucleosome
    
  • 2aro, 1tzy, 1hq3, 2hio, 1hio - cH3 + H4 + H2A + H2B
  • 1eqz - cH3 + H4 + H2A + H2B in nucleosome
    
  • 2pyo, 3nqb, 2nqb - DmH3 + H4 + H2A + H2B in nucleosome
    
  • 6pwe - DmH3 + H4 + H2A + H2B in nucleosome – Cryo EM
    
  • 6pwf - DmH3 + H4 + H2A + H2B in nucleosome + chromatin remodeling factor – Cryo EM
    
  • 5wcu - DmH3 + H4 + H2A + H2B + H5 in nucleosome
    
  • 4x23 - DmH3 + H4 + H2A + H2B in nucleosome + Cenp-C
    
  • 6dzt - DmH3 + H4 + H2A + H2B in nucleosome + antibody
    
  • 6xws, 6xwt - DmH4 + CenP-A + CAL1
    
  • 6j51, 6j50, 6j4z, 6j4y, 6j4x, 6j4w, 6inq, 6i84, 6a5u, 6a5t, 6a5r, 6a5p, 6a5o, 6a5l – yH3.3 + H4 + H2A + H2B in nucleosome + RNA polymerase + RNA – Cryo EM
    
  • 6ir9 – yH3.3 + H4 + H2A + H2B in nucleosome + RNA polymerase + SPT4 + SPT5 + RNA – Cryo EM
    
  • 6gen, 6gej – yH3 + H4 + H2A + H2B in nucleosome + SWI1 + actin-like protein + vacuolar protein sorting-associated + RNA – Cryo EM
    
  • 1id3 - yH3 + H4 + H2A + H2B in nucleosome
    
  • 4jjn, 4kud - yH3 + H4 + H2A.2 + H2B.2 in nucleosome + SIR3
    
  • 5zbb, 5zba - yH3 + H4 + RTT109 + ASF1
    
  • 5z3v, 5z3u, 5z3o, 5z3l - yH3.2 + H4 + H2A + H2B in nucleosome + SNF2 – Cryo EM
    
  • 7k7g - yH3 + H4 + H2A + H2B in nucleosome + CenP-3 – Cryo EM
    
  • 6qld - yH3 + H4 + H2A + H2B in kinetochore + CenP-A – Cryo EM
    
  • 6kxv - H3 + hH4 + hH2A + hH2B in nucleosome – Leishmania major
    
• Chromatosome core + DNA
  • 6la2, 6la8, 6la9, 6lab, 7cow - hH3.1 + H4 + H2A + H2B + H1.0 in chromatosome
    
  • 7dbp - hH3.1 + H4 + H2A + H2B + H1.0 in chromatosome – Cryo EM
    
  • 7k5x, 7k5y, 7k60, 7k61, 7k63 - hH3.1 + H4 + H2A + H2B + H1.0 in chromatosome + scFv – Cryo EM
    
  • 5nl0 - XlH3.2 + H4 + H2A + H2B + H1.0 in chromatosome<br