8X2Y: The class1 of piccolo NuA4
The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state. Determined by electron microscopy at 4.1 Å resolution. Released 19 Mar 2025.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Saccharomyces cerevisiae, Escherichia coli, Schistosoma japonicum
- Chains
- 14
- Atoms
- 17,396
- Mol. weight
- 398.76 kDa
- Released
- 19 Mar 2025
Explore 8X2Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8X2Y contains 69 α-helices and 30 β-strands across 12 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 | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 2 |
| 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 | 45 | 1 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 97 | 1 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-22 | 3 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 50-65 | 16 | |
| α-helix | 66-68 | 3 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-85 | 5 | |
| α-helix | 92-95 | 4 | |
| α-helix | 96-98 | 3 | |
| β-strand | 101-103 | 3 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-50 | 10 | |
| β-strand | 56-57 | 2 | 5 |
| α-helix | 61-86 | 26 | |
| β-strand | 91-92 | 2 | 4 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-126 | 20 | |
Chain E: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83 | 1 | 7 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain F: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-40 | 7 | |
| α-helix | 51-76 | 26 | |
| β-strand | 80 | 1 | 7 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-38 | 11 | |
| β-strand | 43-44 | 2 | 8 |
| α-helix | 50-61 | 12 | |
| α-helix | 64-67 | 4 | |
| α-helix | 69-73 | 5 | |
| β-strand | 78-79 | 2 | 9 |
| α-helix | 81-88 | 8 | |
| β-strand | 102 | 1 | 3 |
| α-helix | 114-116 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 9 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 8 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 19 | |
4 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 | A, E | protein | 136 | Saccharomyces cerevisiae | P61830 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Saccharomyces cerevisiae | P02309 (AlphaFold model) |
| Histone H2A | C, G | protein | 134 | Saccharomyces cerevisiae | Q12692 (AlphaFold model) |
| Histone H2B | D, H | protein | 131 | Saccharomyces cerevisiae | P02293 (AlphaFold model) |
| Histone acetyltransferase | K | protein | 469 | Saccharomyces cerevisiae | Q08649 |
| Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 | L | protein | 537 | Escherichia coli, Saccharomyces cerevisiae | P0AEX9, P47128 |
| glutathione transferase,Enhancer of polycomb-like protein | M | protein | 586 | Schistosoma japonicum, Saccharomyces cerevisiae | P08515, P43572 |
| Chromatin modification-related protein | N | protein | 120 | Saccharomyces cerevisiae | P38806 |
| DNA (146-mer) | I, J | DNA | 146 | Saccharomyces cerevisiae | |
Sequence of entity 1 (A, E), FASTA
>8X2Y_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS
Sequence of entity 2 (B, F), FASTA
>8X2Y_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG
Sequence of entity 3 (C, G), FASTA
>8X2Y_3 Histone H2A (chains C, G)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK
Sequence of entity 4 (D, H), FASTA
>8X2Y_4 Histone H2B (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (K), FASTA
>8X2Y_5 Histone acetyltransferase (chains K)
MGSSHHHHHHSQDHENLYFQGAGSMSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEER
LAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKK
KATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQ
NPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRK
KCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCM
TRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGS
PEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRY
YKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW
Sequence of entity 6 (L), FASTA
>8X2Y_6 Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 (chains L)
MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIK
VTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTW
DAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEP
YFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAE
AAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKE
LAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIP
QMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGIEGRISEFENLY
FQGHMTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHG
GAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND
Sequence of entity 7 (M), FASTA
>8X2Y_7 glutathione transferase,Enhancer of polycomb-like protein (chains M)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLVPRGSENLYFQGHMSSNSR
FRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGH
TKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNE
QVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNL
RNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQ
LKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKR
ENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT
Sequence of entity 8 (N), FASTA
>8X2Y_8 Chromatin modification-related protein (chains N)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
Sequence of entity 9 (I, J), FASTA
>8X2Y_9 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
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 P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
- 7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
- 3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
- 8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
- 2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
- 7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
- 5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
- 7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
- 1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
- 1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
- 2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
- 5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr
Browse structure collections
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