9YLE: State 3 MLL4FC
State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac. Determined by electron microscopy at 3.63 Å resolution. Released 3 Jun 2026.
- Method
- Electron microscopy
- Resolution
- 3.63 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 17
- Atoms
- 26,853
- Mol. weight
- 535.41 kDa
- Released
- 3 Jun 2026
Explore 9YLE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9YLE contains 87 α-helices and 163 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: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 40 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 40 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-92 | 10 | |
| β-strand | 97 | 1 | 41 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-20 | 4 | |
| α-helix | 29-36 | 8 | |
| β-strand | 43 | 1 | 42 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 43 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 44 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-48 | 9 | |
| β-strand | 53-54 | 2 | 43 |
| α-helix | 57-80 | 24 | |
| β-strand | 89 | 1 | 42 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-121 | 17 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 45 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 46 |
| 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 | 46 |
| α-helix | 51-74 | 24 | |
| β-strand | 80-81 | 2 | 45 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 44 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 43 | 1 | 47 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 48 |
| α-helix | 80-85 | 6 | |
| α-helix | 93-95 | 3 | |
| β-strand | 101 | 1 | 41 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-48 | 9 | |
| β-strand | 53-54 | 2 | 48 |
| α-helix | 56-80 | 25 | |
| β-strand | 89 | 1 | 47 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
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 |
|---|
| Ubiquitin | O | protein | 76 | Homo sapiens | P0CG47 (AlphaFold model) |
| [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D | K | protein | 1256 | Homo sapiens | O14686 |
| Retinoblastoma-binding protein 5 | N | protein | 538 | Homo sapiens | Q15291 (AlphaFold model) |
| Set1/Ash2 histone methyltransferase complex subunit ASH2 | T | protein | 628 | Homo sapiens | Q9UBL3 (AlphaFold model) |
| Histone H3.1 | A, E | protein | 135 | Homo sapiens | P68431 |
| 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 (145-mer) | J | DNA | 147 | synthetic construct | |
| WD repeat-containing protein 5 | R | protein | 334 | Homo sapiens | P61964 |
| DNA (145-mer) | I | DNA | 147 | synthetic construct | |
| Protein dpy-30 homolog | P, Q | protein | 99 | Homo sapiens | Q9C005 |
Sequence of entity 1 (O), FASTA
>9YLE_1 Ubiquitin (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC
Sequence of entity 2 (K), FASTA
>9YLE_2 [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D (chains K)
MDYKDDDDKSDTMQNTVVLFSNTDKFVLMQDMCVVCGSFGRGAEGHLLACSQCSQCYHPY
CVNSKITKVMLLKGWRCVECIVCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG
GWKCKWCVSCMQCGAASPGFHCEWQNSYTHCGPCASLVTCPICHAPYVEEDLLIQCRHCE
RWMHAGCESLFTEDDVEQAADEGFDCVSCQPYVVKPAAPVAPPELSNKEDAAARKPLTPK
PKRVQKASDRLVSSRKKLRKEDGVRASEALLKQLKQELSLLPLTEPAITANFSLFAPFGS
GCPVNGQSQLRGAFGSGALPTGPDYYSQLLTKNNLSNPPTPPSSLPPTPPPSVQQKMVNG
VTPSEELGEHPKDAASARDSERALRDTSEVKSLDLLAALPTPPHNQTEDVRMESDEDSDS
PDSIVPASSPESILGEEAPRFPHLGSGRWEQEDRALSPVIPLIPRASIPVFPDTKPYGAL
GLEVPGKLPVTTWEKGKGSEVSVMLTVSAAAAKNLNGVMVAVAELLSMKIPNSYEVLFPE
SPARAGTEPKKGEAEGPGGKEKGLEGKSPDTGPDWLKQFDAVLPGYTLKSQLDILSLLKQ
ESPAPEPPTQHSYTYNVSNLDVRQLSAPPPEEPSPPPSPLAPSPASPPTEPLVELPTEPL
AEPPVPSPLPLASSPESARPKPRARPPEEGEDSRPPRLKKWKGVRWKRLRLLLTIQKGSG
RQEDEREVAEFMEQLGTALRPDKVPRDMRRCCFCHEEGDGATDGPARLLNLDLDLWVHLN
CALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRA
KCMFFKDKTMLCPMHKIKGPCEQELSSFAVFRRVYIERDEVKQIASIIQRGERLHMFRVG
GLVFHAIGQLLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSIGENNGRPEF
VIKVIEQGLEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAV
LRIAESLPGVESCQNYLFRYGRHPLMELPLMINPTGCARSEPKILTHYKRPHTLNSTSMS
KAYQSTFTGETNTPYSKQFVHSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHT
MVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNC
VAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN
Sequence of entity 3 (N), FASTA
>9YLE_3 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL
Sequence of entity 4 (T), FASTA
>9YLE_4 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains T)
MAAAGAGPGQEAGAGPGPGAVANATGAEEGEMKPVAAGAAAPPGEGISAAPTVEPSSGEA
EGGEANLVDVSGGLETESSNGKDTLEGAGDTSEVMDTQAGSVDEENGRQLGEVELQCGIC
TKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYFLRKQANLKEMCLSALANLTWQS
RTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRPGKMTWPNNIVKTMSKERDVFLVKEHP
DPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAVSTSGNLNGGIAAGSSGKGRGAKR
KQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLEL
DCWAGKPIPGDLYRACLYERVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGA
WYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGY
GQGDVLGFYINLPEDTETAKSLPDTYKDKALIKFKSYLYFEEKDFVDKAEKSLKQTPHSE
IIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMGWG
AVVEHTLADVLYHVETEVDGRRSPPWEP
Sequence of entity 5 (A, E), FASTA
>9YLE_5 Histone H3.1 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 6 (B, F), FASTA
>9YLE_6 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (C, G), FASTA
>9YLE_7 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 8 (D, H), FASTA
>9YLE_8 Histone H2B type 2-E (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Sequence of entity 9 (J), FASTA
>9YLE_9 DNA (145-MER) (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 10 (R), FASTA
>9YLE_10 WD repeat-containing protein 5 (chains R)
MATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWL
ASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGK
CLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKL
WDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
TDVVISTACHPTENIIASAALENDKTIKLWKSDC
Sequence of entity 11 (I), FASTA
>9YLE_11 DNA (145-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT
Sequence of entity 12 (P, Q), FASTA
>9YLE_12 Protein dpy-30 homolog (chains P, Q)
MEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQT
VVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN
Primary citation
State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac. Sun, J., Roeder, R. To be published.
Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
- 5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
- 5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
- 4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
- 5GOD 1.15 Å, Lys27-linked di-ubiquitin
- 5GOB 1.15 Å, Lys6-linked di-ubiquitin
- 5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
- 7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
- 8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
- 5DK8 1.32 Å, Human ubiquitin in the P1 space group
- 7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
- 5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
Browse structure collections
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