Histone methyltransferase 3D structures

3D Structures of histone methyltransferase

Updated on 09-September-2025

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• DOT1L histone methyltransferase
  • 1nw3 – hHMT DOT1L – human
• Euchromatic histone methyltransferase
  • 2igq – hHMT-1 C terminal
• Histone-lysine N-methyltransferase; Domains – Tudor 190-410; CxxC or zinc finger 1146-1214
  • 3s8s – hKHMT SETD1A RRM domain
    
  • 2mdc, 2mdj - hKHMT SETD2 WW domain - NMR
    
  • 2mdi - hKHMT SETD2 WW domain (mutant) - NMR
    
  • 3dlm, 5kh6 - hKHMT SETDB1 tudor domain
    
  • 5tfp - hKHMT SETDB2 N-terminal
    
  • 2r3a – hKHMT Suv39H2
    
  • 3rq4 - hKHMT Suv420H2
    
  • 3s8p - hKHMT Suv420H1
    
  • 3mts - hKHMT Suv39H1 chromo domain
    
  • 1h3i - hKHMT SET7/9 residues 52-344
    
  • 2o8j - hKHMT H3K9 residues 913-1193
    
  • 2j2s – Mll1 CxxC domain - NMR
    
  • 5f5e – Mll1 residues 3813-3969
    
  • 5f59 – Mll3 residues 4757-4910
    
  • 2lv9 - hKHMT Mll5 residues 109-188 - NMR
    
  • 5ht6 - Mll5 residues 323-458
    
  • 2kyu - hKHMT Mll Phd3 finger – NMR
    
  • 6g3p, 6g3t - hKHMT Nsd3 residues 247-398
    
  • 4gnd - hKHMT Nsd3 Phd5-C5HCH 1310-1413
    
  • 4rxj - hKHMT Nsd3 residues 953-1064
    
  • 5upd- hKHMT Nsd3 residues 1054-1285
    
  • 3lqh - hKHMT Mll Phd bromodomain
    
  • 3b7b - hKHMT ankyrin repeat domains 2-7
    
  • 3bo5 – hKHMT Setmar methyltransferase domain
    
  • 3k9j, 3k9k – hKHMT Setmar transposable domain (mutant)
    
  • 3n71 - hKHMT Smyd1
    
  • 9ckf, 9ckg - hKHMT Smyd2 (mutant)
    
  • 5hi7 - hKHMT Smyd3
    
  • 3rsn, 3s32 – hKHMT Ash2 N terminal
    
  • 3toj – hKHMT Ash2 Spry domain
    
  • 4ijd – hKHMT Prdm9
    
  • 4mi0 – hKHMT Ezh2
    
  • 4mi5 – hKHMT Ezh2 SET domain
    
  • 6by9 - hKHMT EHMT1 residues 672-999
    
  • 6mm1 - hKHMT EHMT2 Cys-rich domain residues 419-552
    
  • 5v2n - hKHMT KMT5A residues 231-393
    
  • 6xau – mKHMT Prdm3 PR domain - mouse
    
  • 2j8a – KHMT SET1 RRM domain – yeast
    
  • 1u2z – yKHMT C terminal
    
  • 5h6z, 5ww0 - KHMT SET7 – fission yeast
    
  • 1ml9 – NcKHMT Dim-5 – Neurospora crassa
    
  • 1n3j – PvKHMT – Paramecium bursaria chlorella virus
    
  • 2l7p – AtKHMT Ashh2 CW domain – Arabidopsis thaliana - NMR
    
  • 2lxe – AtKHMT Suvr4 SET31 - NMR
    
• Histone-lysine N-methyltransferase binary complexes with DNA
  • 2kkf – hKHMT Hrx CxxC domain + DNA – NMR
    
  • 4nw3 – hKHMT Mll CxxC domain + DNA
    
  • 4pzi – hKHMT CxxC domain + DNA
    
  • 3q0b, 3q0c, 3q0d, 3q0f – hKHMT SRA domain + DNA
    
  • 5vc8 - hKHMT Nsd2 + DNA
    
  • 5egb, 5eh2, 5ei9 - hKHMT Prdm9 zinc finger domain + DNA
    
  • 4ygi – AtKHMT Suvh4 + DNA
    
  • 6a5n – AtKHMT Suvh6 + DNA
    
• Histone-lysine N-methyltransferase binary complexes with methyl donor
  • 4z4p – hKHMT Mll4 SET domain + SAH
    
  • 3qow – hKHMT + SAM
    
  • 4ynm – hKHMT Ash1L + SAM
    
  • 4ynp, 4ypa, 4ype, 4ypu – hKHMT Ash1L (mutant) + SAM
    
  • 4h12, 5jle – hKHMT SETD2 catalytic domain + SAH
    
  • 3smt – hKHMT SETD3 + SAM
    
  • 3ooi, 6kqp - hKHMT Nsd1 SET domain residues 1864-2083 + SAM
    
  • 3qox, 3sx0 – hKHMT + SAH
    
  • 2w5y – hKHMT Hrx methyltransferase domain + SAH
    
  • 3rib, 6n3g – hKHMT Smyd2 + SAH
    
  • 3s7j, 3tg4 - hKHMT Smyd2 + SAM
    
  • 1mt6 - hKHMT SET7/9 residues 58-337 + SAH
    
  • 1n6a – hKHMT SET7/9 SET domain + SAM
    
  • 1n6c – hKHMT SET7/9 residues 70-366 + SAM
    
  • 4bup – mKHMT SET domain 70-336 + SAM
    
  • 6a5k, 6a5m – AtKHMT Suvh6 + SAM
    
• Histone-lysine N-methyltransferase binary complexes with inhibitor
  • 3sr4, 3uwp, 4ek9, 4ekg, 4eki, 4eqz, 4er0, 4er3, 4er5, 4er6, 4er7, 4hra - hKHMT catalytic domain + inhibitor
    
  • 4wuy, 5wcg, 6cbx, 6cby - hKHMT Smyd2 + inhibitor
    
  • 5cpr - hKHMT Suv420 SET domain + inhibitor
    
  • 6p0r - hKHMT Suv39h2 SET domain + inhibitor
    
  • 5w1y, 6boz - hKHMT KMT5A SET domain (mutant) + inhibitor
    
  • 5wbv - hKHMT KMT5B SET domain + inhibitor
    
  • 5vpj, 5vsd, 5vsf - hKHMT EHMT1 SET domain + inhibitor
    
  • 5vpi, 5vsc, 5vse - hKHMT EHMT2 SET domain + inhibitor
    
  • 6nm4 - hKHMT Prdm9 zinc finger domain + inhibitor
    
  • 6ue6, 6xcg - hKHMT Nsd2 PWWP1 domain residues 211-350 + inhibitor
    
  • 6g24, 6g25, 6g27, 6g29, 6g2b, 6g2c, 6g2e, 6g2f, 6g2o - hKHMT Nsd3 residues 247-398 + inhibitor
    
  • 6u9k, 6u9m, 6u9n, 6u9r - hKHMT MLL1 SET 167-333 (mutant) + inhibitor
    
• Histone-lysine N-methyltransferase binary complexes with polypeptide
  • 3f2k – hKHMT Setmar SET domain + LYFA peptide
    
  • 3sw9, 3swc – hKHMT SET domain + peptide
    
  • 4gne, 4gnf, 4gng - hKHMT Nsd3 Phd5-C5HCH + H3 peptide
    
  • 3b95 - hKHMT ankyrin repeat domain + H3 peptide
    
  • 6bhd, 6bhe, 6bhg, 6bhh, 6bhi - hKHMT SETDB1 tudor domain + H3 peptide
    
  • 3lqi, 3lqj - hKHMT Mll1 3rd Phd finger and bromodomain + H3 peptide
    
  • 6mlc - hKHMT Mll3 Phd7 domain + H4 peptide
    
  • 6o7g - hKHMT Mll4 Phd6 domain + H4 peptide - NMR
    
  • 9ckc - hKHMT Smyd2 + peptide
    
  • 5ex0, 5ex3 - hKHMT Smyd3 + peptide
    
  • 5yvx - hKHMT Ashh2 CW domain + H3 peptide
    
  • 6qxz - hKHMT Ashh2 CW domain + H3 peptide - NMR
    
  • 4l58 - hKHMT PHD-type zinc finger domain + H3 peptide
    
  • 6cko - zKHMT + AF-10 - zebrafish
    
• Histone-lysine N-methyltransferase other binary complexes
  • 3cbp - hKHMT SET7/9 SET domain + sinefungin
    
  • 3vuz, 3vv0 - hKHMT SET7/9 SET domain + deoxyadenosine derivative
    
  • 4x8p, 4x8n – hKHMT Ash2L Spry domain + RBBP5
    
  • 4riq, 6e2h – hKHMT SET/Ash2 + DPY-30L
    
  • 6u4y - hKHMT Ezh2 + polycomb protein EED
    
  • 6jn2 – hKHMT4 coiled-coil domain 470-550 + AF-10
    
• Histone-lysine N-methyltransferase ternary complex containing polypeptide
  • 2w5z – hKHMT Hrx methyltransferase domain + SAH + histone peptide
    
  • 5jjy, 5jlb 5v21, 5v22 - hKHMT SETD2 catalytic domain 1434-1711 + SAH + H3 peptide
    
  • 6vdb - hKHMT SETD2 catalytic domain + SAH + peptide
    
  • 6jat, 6ox0, 6ox1, 6ox2, 6ox3, 6ox4, 6ox5 - hKHMT SETD3 + sinefungin + actin peptide
    
  • 6v63, 6wk1, 6wk2 - hKHMT SETD3 + SAH + actin peptide
    
  • 6v62 - hKHMT SETD3 (mutant) + SAH + actin peptide
    
  • 1o9s - hKHMT SET7/9 SET domain + SAH + H3 peptide
    
  • 2bqz - hKHMT SET7 SET domain + SAH + H4 peptide
    
  • 6mbl, 6mbk, 6mbj, 6icv, 6ict - hKHMT SETD3 + SAH + actin peptide
    
  • 3f9w, 3f9x, 3f9y, 3f9z - hKHMT SETD8 SET domain + SAH + H4 peptide
    
  • 5teg - hKHMT SETD8 SET domain + SAM + H4 peptide
    
  • 5eg2 - hKHMT SETD7 SET domain + SAH + TAF10 peptide
    
  • 4ij8 - hKHMT SETD8 + SAM + H3 peptide
    
  • 4j7f, 4j7i, 4j83, 4j8o - hKHMT SETD7 + SAH + TFIID peptide
    
  • 2rfi, 3hna - hKHMT H3K9 catalytic domain + SAH + H3 peptide
    
  • 1xqh - hKHMT SET7/9 SET domain + SAH + p53 peptide
    
  • 2f69, 3m53 - hKHMT SET7/9 SZET domain + SAH + TAF10 peptide
    
  • 3m54, 3m55, 3m56, 3m57, 3m58, 3m59, 3m5a - hKHMT SET7/9 SET domain (mutant) + SAH + TAF10 peptide
    
  • 3cbm - hKHMT SET7/9 SET domain + SAM + estrogen receptor peptide
    
  • 3cbo - hKHMT SET7/9 SET domain + SAH + estrogen receptor peptide
    
  • 3os5 - hKHMT SET7/9 SET domain + SAH + DNMT1 peptide
    
  • 3qxy, 3rc0 - hKHMT SETD6 SET domain + p65 peptide + SAM
    
  • 5jhn, 5jin, 5jiy, 5jj0 - hKHMT EHMT2 SET domain + SAM + H3 peptide
    
  • 3s7d, 3s7f, 3tg5 - hKHMT Smyd2 + SAH + p53 peptide
    
  • 4o6f – hKHMT Smyd2 (mutant) + SAH + estrogen receptor peptide
    
  • 5v3h – hKHMT Smyd2 (mutant) + SAM + inhibitor
    
  • 5v37, 6p6k, 6p7z, 6paf – hKHMT Smyd3 + SAM + inhibitor
    
  • 6o9o, 6p6g – hKHMT Smyd3 + SAH + inhibitor
    
  • 5hq8 – hKHMT Smyd3 + SAH + MEKK2 peptide
    
  • 6ago, 6ine – hKHMT Ash1L + MRG15 + SAM
    
  • 1zkk - hKHMT + SAH + H4 peptide
    
  • 4c1q - hKHMT SET domain + SAH + H3 peptide
    
  • 4i51 - hKHMT (mutant) + SAH + H3 peptide
    
  • 6cen - hKHMT Nsd3 + inhibitor peptide + SAM
    
  • 7bre – hKHMT Mll1 + RBBP5 + Ash2L
    
  • 5f6l, 7w67, 7w6a, 7w6i, 7w6j – hKHMT Mll1 (mutant) + RBBP5 + Ash2L
    
  • 5f6k – hKHMT Mll3 + RBBP5 + Ash2L + peptide
    
  • 1peg - NcKHMT Dim-5 + SAH + H3 peptide
    
  • 2g46 – PvKHMT + SAH + H3 peptide
    
  • 4au7 - mKHMT + SAH + H4 peptide
    
• Histone-lysine N-methyltransferase ternary complex containing inhibitor; Domains – catalytic 879-1159; SET 1006-1266
  • 4e47, 4jds, 4jlg, 5ayf - hKHMT SET7/9 SET domain + SAM + inhibitor
    
  • 5ylt - hKHMT SET7/9 SET domain + sinefungin + inhibitor
    
  • 3fpd, 3k5k, 3mo0, 3mo2, 3mo5, 3rjw, 4nvq - hKHMT SET domain + SAH + inhibitor
    
  • 7lzb, 7lzd, 7lzf - hKHMT SETD2 catalytic domain 1434-1711 + SAH + inhibitor
    
  • 5tuz, 6mbo, 6mbp - hKHMT EHMT1 SET domain + SAH + inhibitor
    
  • 5ttg, 5v9j - hKHMT EHMT1 catalytic domain + SAM + inhibitor
    
  • 5tuy, 5v9i, 7btv, 7buc, 7dcf - hKHMT EHMT2 SET domain + SAM + inhibitor
    
  • 5ttf - hKHMT EHMT2 catalytic domain + SAM + inhibitor
    
  • 3s7b, 4ynd, 5arf, 5arg, 5kjk, 5kjl, 5kjm, 5kjn - hKHMT Smyd2 + SAM + inhibitor
    
  • 6mon - hKHMT Smyd2 + SAH + inhibitor peptide
    
  • 5ccl, 5ccm, 5xxd, 5xxg, 5xxj, 5yjo, 6ijl – hKHMT Smyd3 + SAM + inhibitor
    
  • 1zkk - hKHMT + SAH + H4 peptide
    
  • 6in3 – hKHMT DOT1L + SAH + inhibitor
    
  • 6kqq - hKHMT Nsd1 SET domain residues 1864-2083 + SAM + inhibitor
    
  • 6nm4 - hKHMT Prdm9 zinc finger domain + inhibitor + SAM
    
  • 6wzw – hKHMT Ash1L SET domain 2074-2293 + inhibitor + SAM
    
  • 6x0p – hKHMT Ash1L SET domain 2074-2293 (mutant) + inhibitor + SAM
    
  • 6w5i, 6w5m, 6w5n – hKHMT Ash2L in nucleosome – Cryo EM
    
  • 7ea8 – hKHMT Setd2 in nucleosome – Cryo EM
    
  • 4qen, 4qeo, 4qep – AtKHMT Suvh4 + DNA + SAH
    
• Histone-lysine N-methyltransferase higher complexes
  • 5hq2 - hKHMT SETD8 SET domain + H3 + H4 + H2 + SRM1 + DNA
    
  • 6jm9 - hKHMT DOT1 + H3.2 + H4 + H2A + H2B + DNA – Cryo EM
    
  • 6j99, 6jm9, 6jma, 6nj9, 6nn6, 6nog, 6nqa, 6o96, 7bwd, 7k6p, 7k6q - hKHMT DOT1 in nucleosome – Cryo EM
    
  • 7cro - hKHMT Nsd2 in nucleosome – Cryo EM
    
  • 7crr - hKHMT Nsd3 in nucleosome – Cryo EM
    
  • 7crp, 7crq - hKHMT Nsd3 (mutant) in nucleosome – Cryo EM
    
  • 6w5i, 6w5m, 6w5n – hKHMT Ash2L in nucleosome – Cryo EM
    
  • 7xpx – hKHMT SET8 in nucleosome – Cryo EM
    
  • 7mbm, 7mbn, 7ud5 – hKHMT MLL1 in nucleosome – Cryo EM
    
  • 5t0k, 5t0m - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide
    
  • 5hyn, 5ls6 - hKHMT Ezh2in+ polycomb complex + inhibitor
    
  • 6c23, 6c24, 6wkr - hKHMT Ezh2 in polycomb complex – Cryo EM
    
  • 7kso, 7ksr, 7ktp - hKHMT Ezh1 in polycomb complex – Cryo EM
    
  • 6pwv - hKHMT 2A + MLL1 complex – Cryo EM
    
  • 6pww - hKHMT 2A + MLL1 complex + RBPP5 + WDR5 – Cryo EM
    
  • 6kiu, 6kiv - hKHMT 2A + MLL1-UBNCP complex – Cryo EM
    
  • 6kiw - hKHMT 2A + MLL3-UBNCP complex – Cryo EM
    
  • 6kix, 6kiz - hKHMT 2A + MLL1-NCP complex – Cryo EM
    
  • 6nzo, 6px3, 6ugm, 6uh5 - fKHMT in nucleosome – frog – Cryo EM
    
  • 6uh5 - fKHMT in nucleosome + ubiquitin – Cryo EM
    
  • 6ven - yKHMT 762-1080 in compass complex – Cryo EM
    
  • 7ea5 - yKHMT in nucleosome – Cryo EM
    
• Histone-arginine N-methyltransferase (Carm1)
  • 4qqk – hPRMT6
    
  • 4hc4 – hPRMT6 (mutant)
    
  • 2v74, 2v7e – mPRMT catalytic domain
    
  • 4c03, 4c06, 4c07, 4c08, 5hzm, 6sqh, 6sqi – mPRMT6
    
  • 2obq – rPRMT N terminal - rat
    
  • 3b3g, 3b3j – rPRMT catalytic domain
    
• Histone-arginine N-methyltransferase (Carm1) binary complex
  • 5u4x – hPRMT1 catalytic domain + SAH
    
  • 6nt2 – hPRMT1 residues 1-371 + inhibitor
    
  • 5dxj – hPRMT4 catalytic domain 145-489 + sinefungin
    
  • 4ikp, 6d2l, 6dvr – hPRMT4 catalytic domain + purine derivative
    
  • 6izq, 6s70, 6s71, 6s74, 6s77, 6s79, 6s7a, 6s7b, 6s7c, 6te6, 6tel, 6ten – hPRMT4 catalytic domain + inhibitor
    
  • 7boc – hPRMT5 TIM barrel domain 1-292 + peptide
    
  • 6ugh – hPRMT5 + MEP50 – Cryo EM
    
  • 5egs, 5lv2, 5lv3, 5lv4, 5lv5, 5wcf – hPRMT6 + inhibitor
    
  • 5dst – hPRMT8 catalytic domain + SAH
    
  • 5ih3 – mPRMT4 + SAH
    
  • 5isi, 5is6, 5is7, 5is8, 5is9, 5isa, 5isb, 5isc, 5isd, 5ise, 5isf, 5isg, 5ish, 5k8v, 5k8w, 5k8x, 5lkj, 5ntc, 5tbh, 5tbi, 5tbj – mPRMT4 + inhibitor
    
  • 5lgp, 5lgq, 5lgr, 5lgs – mPRMT4 + poly(A)-binding protein peptide + inhibitor
    
  • 4c04, 6sq3, 6sq4, 7nud, 7nue, 7p2r, 7ppq, 7ppy, 7pu8, 7puc, 7puq, 7pv6 – mPRMT 6 + inhibitor
    
  • 6sqk – mPRMT 6 + peptide
    
  • 7os4 – mPRMT 6 + histone H3.1
    
  • 7okp – mPRMT 6 + histone H3.3
    
  • 4c05, 5fqn, 5fqo – mPRMT6 + SAH
    
  • 4c4a – mPRMT7 + SAH
    
  • 6ogn – mPRMT7 + inhibitor
    
  • 3b3f – rPRMT catalytic domain + SAH
    
  • 6z2a – fyPRMT (mutant) + SAH – fission yeast
    
  • 6bp4 – fyPRMT catalytic domain + SAH
    
• Histone-arginine N-methyltransferase (Carm1) ternary complex
  • 5dx1, 5dx8, 5dxa – hPRMT4 catalytic domain + sinefungin + peptide
    
  • 5dwq, 5dx0 – hPRMT4 catalytic domain + sinefungin + H3 peptide
    
  • 2y1w, 2y1x – hPRMT4 catalytic domain + sinefungin + indole inhibitor
    
  • 6arj, 6arv – hPRMT4 catalytic domain + SAH + inhibitor
    
  • 6rll, 6rlq, 6uxx, 6uxy – hPRMT5 + MEP50 + inhibitor
    
  • 7m05 – hPRMT5 + MEP50 + inhibitor – Cryo EM
    
  • 6w6d, 6wad, 7nr4 – hPRMT6 1-375 + SAH + inhibitor
    
  • 5lgp, 5lgq, 5lgr, 5lgs – mPRMT 4 + poly(A)-binding protein peptide + inhibitor
    
  • 4gqb, 5fa5 – hPRMT5 + MEP50 + H4 peptide
    
  • 5emm – hPRMT5 + MEP50 + sinefungin
    
  • 6k1s, 7kic – hPRMT5 + MEP50 + inhibitor
    
  • 5eml, 7kib, 7l1g – hPRMT5 + MEP50 + SAM
    
  • 5c9z, 5emj, 5emk – hPRMT5 + MEP50 + sinefungin + inhibitor
    
  • 6v0n, 6v0o – hPRMT5 + MEP50 + sinefungin + peptide
    
  • 4x60, 4x61, 4x63 – hPRMT5 + MEP50 + SAH + inhibitor
    
  • 6ckc, 7kid – hPRMT5 + MEP50 + inhibitor
    
  • 4y2h, 4y30, 5e8r, 6p7i – hPRMT6 + SAH + inhibitor
    
  • 4qpp – hPRMT6 (mutant) + peptide + inhibitor
    

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Michal Harel, Joel L. Sussman