Histone methyltransferase 3D structures

From Proteopedia

3D Structures of histone methyltransferase

Updated on 22-May-2023

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

6g3t, 6g3p - 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

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

5ei9, 5eh2, 5egb - 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

4ypu, 4ype, 4ypa, 4ynp – 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

5mw4, 5mw3, 5mvs, 5juw, 5dtr, 5dtq, 5dtm, 5dt2, 5dsx, 5dry, 5drt, 4wvl – hKHMT DOT1L + inhibitor

4fmu, 5lt8, 5lt7, 5lt6, 5lsz, 5lsy, 5lsx, 5lsu, 5lss – hKHMT SETD2 + inhibitor

5th7 – hKHMT SETD8 + inhibitor

5t5g – hKHMT SETD8 (mutant) + inhibitor

5ke3, 5ke2, 5kco, 5kch, 6bpi, 6au3, 6au2, 7c9n, 7caj, 7cd9, 7cjt - hKHMT SETDB1 tudor domain + inhibitor

3sr4, 3uwp, 4ek9, 4ekg, 4eki, 4eqz, 4er0, 4er3, 4er5, 4er6, 4er7, 4hra - hKHMT catalytic domain + inhibitor

4wuy, 6cby, 6cbx, 5wcg - 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

5vsf, 5vsd, 5vpj - hKHMT EHMT1 SET domain + inhibitor

5vse, 5vsc, 5vpi - hKHMT EHMT2 SET domain + inhibitor

6nm4 - hKHMT Prdm9 zinc finger domain + inhibitor

6ue6, 6xcg - hKHMT Nsd2 PWWP1 domain residues 211-350 + inhibitor

6g2o, 6g2f, 6g2e, 6g2c, 6g2b, 6g29, 6g27, 6g25, 6g24 - 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

6bhi, 6bhh, 6bhg, 6bhe, 6bhd - 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

5ex3, 5ex0 - 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

5v22, 5v21, 5jlb, 5jjy - 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

4j7i, 4j83, 4j8o, 4j7f - 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

5jj0, 5jiy, 5jin, 5jhn - 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

6ine, 6ago – 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, 6mbp, 6mbo - 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, 5kjn, 5kjm, 5kjl, 5kjk, 5arg, 5arf, 4ynd - hKHMT Smyd2 + SAM + inhibitor

6mon - hKHMT Smyd2 + SAH + inhibitor peptide

5ccm, 5ccl, 5yjo, 5xxj, 5xxg, 5xxd, 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

6o96, 6nqa, 6nog, 6nn6, 6nj9, 6jm9, 6jma, 6j99, 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

5t0m, 5t0k - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide

5ls6, 5hyn - hKHMT Ezh2in+ polycomb complex + inhibitor

6c24, 6c23, 6wkr - hKHMT Ezh2 in polycomb complex – Cryo EM

7kso, 7ktp, 7ksr - 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, 5wcf, 5lv5, 5lv4, 5lv3, 5lv2 – hPRMT6 + inhibitor

5dst – hPRMT8 catalytic domain + SAH

5ih3 – mPRMT4 + SAH

5k8v, 5isi, 5ish, 5isg, 5isf, 5ise, 5isd, 5isc, 5isb, 5isa, 5is9, 5is8, 5is7, 5is6, 5tbj, 5tbi, 5tbh, 5ntc, 5lkj, 5k8x, 5k8w – mPRMT4 + inhibitor

5lgs, 5lgr, 5lgq, 5lgp – 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, 5fqo, 5fqn – 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

5dxa, 5dx8, 5dx1 – hPRMT4 catalytic domain + sinefungin + peptide

5dx0, 5dwq – hPRMT4 catalytic domain + sinefungin + H3 peptide

2y1w, 2y1x – hPRMT4 catalytic domain + sinefungin + indole inhibitor

6arv, 6arj – 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

5lgs, 5lgr, 5lgq, 5lgp – 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

5emk, 5emj, 5c9z – hPRMT5 + MEP50 + sinefungin + inhibitor

6v0n, 6v0o – hPRMT5 + MEP50 + sinefungin + peptide

4x63, 4x61, 4x60 – hPRMT5 + MEP50 + SAH + inhibitor

6ckc, 7kid – hPRMT5 + MEP50 + inhibitor

5e8r, 4y30, 4y2h, 6p7i – hPRMT6 + SAH + inhibitor

4qpp – hPRMT6 (mutant) + peptide + inhibitor