8X30: Piccolo NuA4 and H2A.Z nucleosome 2:1 complex
Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex. Determined by electron microscopy at 4.3 Å resolution. Released 19 Mar 2025.
- Method
- Electron microscopy
- Resolution
- 4.3 Å
- Organisms
- Saccharomyces cerevisiae, Schistosoma japonicum, Escherichia coli
- Chains
- 17
- Atoms
- 21,579
- Mol. weight
- 537.3 kDa
- Released
- 19 Mar 2025
Explore 8X30 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8X30 contains 82 α-helices and 23 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, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 64-76 | 13 | |
| α-helix | 86-112 | 27 | |
| α-helix | 121-130 | 10 | |
Chain B: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| α-helix | 50-75 | 26 | |
| α-helix | 84-93 | 10 | |
| β-strand | 98 | 1 | 6 |
Chain C: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 29-38 | 10 | |
| α-helix | 52-64 | 13 | |
| α-helix | 66-70 | 5 | |
| α-helix | 71-74 | 4 | |
| β-strand | 78 | 1 | 7 |
| α-helix | 81-86 | 6 | |
| α-helix | 92-95 | 4 | |
| β-strand | 102 | 1 | 8 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-49 | 9 | |
| β-strand | 56 | 1 | 7 |
| α-helix | 61-86 | 26 | |
| α-helix | 94-103 | 10 | |
| α-helix | 107-124 | 18 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| α-helix | 86-113 | 28 | |
| α-helix | 121-130 | 10 | |
Chain F: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-37 | 4 | |
| α-helix | 51-76 | 26 | |
| α-helix | 83-92 | 10 | |
| β-strand | 97 | 1 | 8 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-38 | 11 | |
| α-helix | 50-74 | 25 | |
| β-strand | 78 | 1 | 9 |
| α-helix | 81-88 | 8 | |
| α-helix | 92-95 | 4 | |
| α-helix | 96-98 | 3 | |
| β-strand | 103 | 1 | 6 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56 | 1 | 9 |
| α-helix | 59-86 | 28 | |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 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 acetyltransferase | K, O | protein | 469 | Saccharomyces cerevisiae | Q08649 (AlphaFold model) |
| glutathione transferase,Enhancer of polycomb-like protein | M, Q | protein | 586 | Schistosoma japonicum, Saccharomyces cerevisiae | P43572 (AlphaFold model), Q540A3 (AlphaFold model) |
| Chromatin modification-related protein | N, R | protein | 120 | Saccharomyces cerevisiae | P38806 (AlphaFold model) |
| Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 | P | protein | 537 | Escherichia coli, Saccharomyces cerevisiae | P47128 |
| DNA (146-mer) | I, J | DNA | 146 | Saccharomyces cerevisiae | |
| Histone H3 | A, E | protein | 136 | Saccharomyces cerevisiae | P61830 |
| Histone H4 | B, F | protein | 102 | Saccharomyces cerevisiae | P02309 |
| Histone H2A | C, G | protein | 134 | Saccharomyces cerevisiae | Q12692 |
| Histone H2B | D, H | protein | 131 | Saccharomyces cerevisiae | P02293 |
Sequence of entity 1 (K, O), FASTA
>8X30_1 Histone acetyltransferase (chains K, O)
MGSSHHHHHHSQDHENLYFQGAGSMSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEER
LAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKK
KATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQ
NPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRK
KCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCM
TRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGS
PEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRY
YKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW
Sequence of entity 2 (M, Q), FASTA
>8X30_2 glutathione transferase,Enhancer of polycomb-like protein (chains M, Q)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLVPRGSENLYFQGHMSSNSR
FRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGH
TKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNE
QVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNL
RNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQ
LKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKR
ENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT
Sequence of entity 3 (N, R), FASTA
>8X30_3 Chromatin modification-related protein (chains N, R)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
Sequence of entity 4 (P), FASTA
>8X30_4 Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 (chains P)
MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIK
VTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTW
DAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEP
YFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAE
AAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKE
LAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIP
QMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGIEGRISEFENLY
FQGHMTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHG
GAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND
Sequence of entity 5 (I, J), FASTA
>8X30_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Sequence of entity 6 (A, E), FASTA
>8X30_6 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS
Sequence of entity 7 (B, F), FASTA
>8X30_7 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG
Sequence of entity 8 (C, G), FASTA
>8X30_8 Histone H2A (chains C, G)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK
Sequence of entity 9 (D, H), FASTA
>8X30_9 Histone H2B (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Primary citation
Cryo-EM structures reveal the acetylation process of piccolo NuA4. Wang, L., Zhang, H., Jia, Q. et al. Proc Natl Acad Sci U S A (2025) 122:e2414490122-e2414490122. DOI 10.1073/pnas.2414490122 · PubMed
Other PDB entries of the same protein (UniProt Q08649 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TO7 1.9 Å, Crystal structure of yeast Esa1 HAT domain bound to coenzyme A with active site lysine…
- 1FY7 2.0 Å, Crystal structure of yeast ESA1 histone acetyltransferase domain complexed with coenzyme a
- 3TO9 2.0 Å, Crystal structure of yeast Esa1 E338Q HAT domain bound to coenzyme A with active site…
- 3TO6 2.1 Å, Crystal structure of yeast Esa1 HAT domain complexed with H4K16CoA bisubstrate inhibitor
- 1MJA 2.26 Å, Crystal structure of yeast Esa1 histone acetyltransferase domain complexed with acetyl…
- 1MJ9 2.5 Å, Crystal structure of yeast Esa1(C304S) mutant complexed with Coenzyme A
- 1MJB 2.5 Å, Crystal structure of yeast Esa1 histone acetyltransferase E338Q mutant complexed with…
- 5J9T 2.7 Å, Crystal structure of the NuA4 core complex
- 5J9W 2.8 Å, Crystal structure of the NuA4 core complex
- 5J9U 2.95 Å, Crystal structure of the NuA4 core complex
- 5J9Q 3.25 Å, Crystal structure of the NuA4 core complex
- 7VVU 3.4 Å, NuA4 HAT module bound to the nucleosome
Browse structure collections
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