9YL3: State 1 MLL4FC

State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac. Determined by electron microscopy at 3.5 Å resolution. Released 3 Jun 2026.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 17
Atoms: 26,713
Mol. weight: 535.44 kDa
Released: 3 Jun 2026

Explore 9YL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YL3 contains 95 α-helices and 165 β-strands across 15 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	25
α-helix	86-113	28
β-strand	118-119	2	26
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	26
α-helix	49-75	27
β-strand	80-81	2	25
α-helix	83-92	10
β-strand	97-98	2	27

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	29-36	8
β-strand	43	1	28
α-helix	47-72	26
β-strand	77-78	2	29
α-helix	80-88	9
α-helix	93-96	4
β-strand	101	1	30
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-46	9
β-strand	53-54	2	29
α-helix	56-83	28
β-strand	89	1	28
α-helix	91-101	11
α-helix	105-122	18

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	31
α-helix	86-113	28
β-strand	118-119	2	32
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	32
α-helix	51-75	25
β-strand	80-81	2	31
α-helix	83-92	10
β-strand	97	1	30

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-36	9
β-strand	43	1	33
α-helix	46-71	26
β-strand	77-78	2	34
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	27
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-46	9
β-strand	53-54	2	34
α-helix	56-83	28
β-strand	89	1	33
α-helix	91-101	11
α-helix	105-123	19

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
[histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D	K	protein	1256	Homo sapiens	A0A6P6IDI8, O14686
Ubiquitin	O	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Histone H3.1	A, E	protein	135	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805
Histone H2A type 1-B/E	C, G	protein	129	Homo sapiens	P04908
Histone H2B type 2-E	D, H	protein	125	Homo sapiens	Q16778
DNA	J	DNA	147	synthetic construct
Retinoblastoma-binding protein 5	N	protein	538	Homo sapiens	Q15291
Set1/Ash2 histone methyltransferase complex subunit ASH2	T	protein	628	Homo sapiens	Q9UBL3
Protein dpy-30 homolog	P, Q	protein	99	Homo sapiens	Q9C005
WD repeat-containing protein 5	R	protein	334	Homo sapiens	P61964
DNA	I	DNA	147	synthetic construct

Sequence of entity 1 (K), FASTA

>9YL3_1 [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D (chains K)
MDYKDDDDKSDTMQNTVVLFSNTDKFVLMQDMCVVCGSFGRGAEGHLLACSQCSQCYHPY
CVNSKITKVMLLKGWRCVECIVCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG
GWKCKWCVSCMQCGAASPGFHCEWQNSYTHCGPCASLVTCPICHAPYVEEDLLIQCRHCE
RWMHAGCESLFTEDDVEQAADEGFDCVSCQPYVVKPVAPVAPPELSNKEDAAARKPLTPK
PKRVQKASDRLVSSRKKLRKEDGVRASEALLKQLKQELSLLPLTEPAITANFSLFAPFGS
GCPVNGQSQLRGAFGSGALPTGPDYYSQLLTKNNLSNPPTPPSSLPPTPPPSVQQKMVNG
VTPSEELGEHPKDAASARDSERALRDTSEVKSLDLLAALPTPPHNQTEDVRMESDEDSDS
PDSIVPASSPESILGEEAPRFPHLGSGRWEQEDRALSPVIPLIPRASIPVFPDTKPYGAL
GLEVPGKLPVTTWEKGKGSEVSVMLTVSAAAAKNLNGVMVAVAELLSMKIPNSYEVLFPE
SPARAGTEPKKGEAEGPGGKEKGLEGKSPDTGPDWLKQFDAVLPGYTLKSQLDILSLLKQ
ESPAPEPPTQHSYTYNVSNLDVRQLSAPPPEEPSPPPSPLAPSPASPPTEPLVELPTEPL
AEPPVPSPLPLASSPESARPKPRARPPEEGEDSRPPRLKKWKGVRWKRLRLLLTIQKGSG
RQEDEREVAEFMEQLGTALRPDKVPRDMRRCCFCHEEGDGATDGPARLLNLDLDLWVHLN
CALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRA
KCMFFKDKTMLCPMHKIKGPCEQELSSFAVFRRVYIERDEVKQIASIIQRGERLHMFRVG
GLVFHAIGQLLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSIGENNGRPEF
VIKVIEQGLEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAV
LRIAESLPGVESCQNYLFRYGRHPLMELPLMINPTGCARSEPKILTHYKRPHTLNSTSMS
KAYQSTFTGETNTPYSKQFVHSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHT
MVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNC
VAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN

Sequence of entity 2 (O), FASTA

>9YL3_2 Ubiquitin (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 3 (A, E), FASTA

>9YL3_3 Histone H3.1 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>9YL3_4 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>9YL3_5 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 6 (D, H), FASTA

>9YL3_6 Histone H2B type 2-E (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 7 (J), FASTA

>9YL3_7 DNA (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 8 (N), FASTA

>9YL3_8 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL

Sequence of entity 9 (T), FASTA

>9YL3_9 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains T)
MAAAGAGPGQEAGAGPGPGAVANATGAEEGEMKPVAAGAAAPPGEGISAAPTVEPSSGEA
EGGEANLVDVSGGLETESSNGKDTLEGAGDTSEVMDTQAGSVDEENGRQLGEVELQCGIC
TKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYFLRKQANLKEMCLSALANLTWQS
RTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRPGKMTWPNNIVKTMSKERDVFLVKEHP
DPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAVSTSGNLNGGIAAGSSGKGRGAKR
KQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLEL
DCWAGKPIPGDLYRACLYERVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGA
WYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGY
GQGDVLGFYINLPEDTETAKSLPDTYKDKALIKFKSYLYFEEKDFVDKAEKSLKQTPHSE
IIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMGWG
AVVEHTLADVLYHVETEVDGRRSPPWEP

Sequence of entity 10 (P, Q), FASTA

>9YL3_10 Protein dpy-30 homolog (chains P, Q)
MEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQT
VVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN

Sequence of entity 11 (R), FASTA

>9YL3_11 WD repeat-containing protein 5 (chains R)
MATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWL
ASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGK
CLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKL
WDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
TDVVISTACHPTENIIASAALENDKTIKLWKSDC

Sequence of entity 12 (I), FASTA

>9YL3_12 DNA (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Primary citation

State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac. Sun, J., Roeder, R. To be published.

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