9YM8: State 2 focused on PHD FYR of MLL4FC
State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac. Determined by electron microscopy at 3.43 Å resolution. Released 3 Jun 2026.
- Method
- Electron microscopy
- Resolution
- 3.43 Å
- Organisms
- synthetic construct, Homo sapiens
- Chains
- 18
- Atoms
- 28,174
- Mol. weight
- 545.27 kDa
- Ligands
- SAH, ZN
- Released
- 3 Jun 2026
Explore 9YM8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9YM8 contains 93 α-helices and 172 β-strands across 16 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 | 46-56 | 11 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 6 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 6 |
| α-helix | 51-75 | 25 | |
| β-strand | 80-81 | 2 | 5 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 7 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 43 | 1 | 8 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 10 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-33 | 3 | |
| α-helix | 40-48 | 9 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 56-83 | 28 | |
| β-strand | 89 | 1 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 11 |
| α-helix | 40-42 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 12 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 12 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 10 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 43 | 1 | 13 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 14 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 7 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 14 |
| α-helix | 56-83 | 28 | |
| β-strand | 89 | 1 | 13 |
| 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 |
|---|
| DNA (145-mer) | I | DNA | 147 | synthetic construct | |
| DNA (145-mer) | J | DNA | 147 | synthetic construct | |
| Ubiquitin | O, U | 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 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 129 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 2-E | D, H | protein | 125 | Homo sapiens | Q16778 |
| WD repeat-containing protein 5 | R | protein | 334 | Homo sapiens | P61964 |
| Retinoblastoma-binding protein 5 | N | protein | 538 | Homo sapiens | Q15291 |
| [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D | K | protein | 1256 | Homo sapiens | O14686 |
| Set1/Ash2 histone methyltransferase complex subunit ASH2 | T | protein | 628 | Homo sapiens | Q9UBL3 |
| Protein dpy-30 homolog | P, Q | protein | 99 | Homo sapiens | Q9C005 |
Sequence of entity 1 (I), FASTA
>9YM8_1 DNA (145-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT
Sequence of entity 2 (J), FASTA
>9YM8_2 DNA (145-MER) (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 3 (O, U), FASTA
>9YM8_3 Ubiquitin (chains O, U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC
Sequence of entity 4 (A, E), FASTA
>9YM8_4 Histone H3.1 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 5 (B, F), FASTA
>9YM8_5 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 6 (C, G), FASTA
>9YM8_6 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 7 (D, H), FASTA
>9YM8_7 Histone H2B type 2-E (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Sequence of entity 8 (R), FASTA
>9YM8_8 WD repeat-containing protein 5 (chains R)
MATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWL
ASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGK
CLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKL
WDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
TDVVISTACHPTENIIASAALENDKTIKLWKSDC
Sequence of entity 9 (N), FASTA
>9YM8_9 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL
Sequence of entity 10 (K), FASTA
>9YM8_10 [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 11 (T), FASTA
>9YM8_11 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains T)
MAAAGAGPGQEAGAGPGPGAVANATGAEEGEMKPVAAGAAAPPGEGISAAPTVEPSSGEA
EGGEANLVDVSGGLETESSNGKDTLEGAGDTSEVMDTQAGSVDEENGRQLGEVELQCGIC
TKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYFLRKQANLKEMCLSALANLTWQS
RTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRPGKMTWPNNIVKTMSKERDVFLVKEHP
DPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAVSTSGNLNGGIAAGSSGKGRGAKR
KQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLEL
DCWAGKPIPGDLYRACLYERVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGA
WYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGY
GQGDVLGFYINLPEDTETAKSLPDTYKDKALIKFKSYLYFEEKDFVDKAEKSLKQTPHSE
IIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMGWG
AVVEHTLADVLYHVETEVDGRRSPPWEP
Sequence of entity 12 (P, Q), FASTA
>9YM8_12 Protein dpy-30 homolog (chains P, Q)
MEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQT
VVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
| ZN | Zinc ion | Zn | 8 |
Primary citation
State 2 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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