8X31: The piccolo NuA4
The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state. Determined by electron microscopy at 6.2 Å resolution. Released 19 Mar 2025.
- Method
- Electron microscopy
- Resolution
- 6.2 Å
- Organisms
- Escherichia coli, Saccharomyces cerevisiae, Schistosoma japonicum
- Chains
- 14
- Atoms
- 16,944
- Mol. weight
- 398.76 kDa
- Released
- 19 Mar 2025
Explore 8X31 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8X31 contains 68 α-helices and 25 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: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-55 | 10 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 51-74 | 24 | |
| β-strand | 80-81 | 2 | 5 |
| α-helix | 84-93 | 10 | |
| β-strand | 97 | 1 | 6 |
Chain C: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 44 | 1 | 7 |
| α-helix | 47-52 | 6 | |
| α-helix | 57-65 | 9 | |
| α-helix | 70-72 | 3 | |
| α-helix | 81-86 | 6 | |
| α-helix | 93-95 | 3 | |
| α-helix | 97-100 | 4 | |
| β-strand | 101 | 1 | 8 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-50 | 10 | |
| α-helix | 61-85 | 25 | |
| β-strand | 92 | 1 | 7 |
| α-helix | 95-103 | 9 | |
| α-helix | 107-125 | 19 | |
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 | 121-131 | 11 | |
Chain F: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-37 | 4 | |
| α-helix | 51-75 | 25 | |
| α-helix | 84-93 | 10 | |
| β-strand | 96 | 1 | 8 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-35 | 8 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 51-69 | 19 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-83 | 3 | |
| α-helix | 84-88 | 5 | |
| α-helix | 92-95 | 4 | |
| α-helix | 96-98 | 3 | |
| β-strand | 102 | 1 | 6 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 10 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 9 |
| 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 |
|---|
| Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 | L | protein | 537 | Escherichia coli, Saccharomyces cerevisiae | P47128 (AlphaFold model) |
| Chromatin modification-related protein | N | protein | 120 | Saccharomyces cerevisiae | P38806 (AlphaFold model) |
| Histone acetyltransferase | K | protein | 469 | Saccharomyces cerevisiae | Q08649 (AlphaFold model) |
| glutathione transferase,Enhancer of polycomb-like protein | M | protein | 586 | Schistosoma japonicum, Saccharomyces cerevisiae | P43572 (AlphaFold model), Q540A3 |
| 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 (L), FASTA
>8X31_1 Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 (chains L)
MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIK
VTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTW
DAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEP
YFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAE
AAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKE
LAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIP
QMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGIEGRISEFENLY
FQGHMTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHG
GAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND
Sequence of entity 2 (N), FASTA
>8X31_2 Chromatin modification-related protein (chains N)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
Sequence of entity 3 (K), FASTA
>8X31_3 Histone acetyltransferase (chains K)
MGSSHHHHHHSQDHENLYFQGAGSMSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEER
LAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKK
KATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQ
NPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRK
KCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCM
TRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGS
PEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRY
YKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW
Sequence of entity 4 (M), FASTA
>8X31_4 glutathione transferase,Enhancer of polycomb-like protein (chains M)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLVPRGSENLYFQGHMSSNSR
FRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGH
TKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNE
QVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNL
RNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQ
LKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKR
ENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT
Sequence of entity 5 (I, J), FASTA
>8X31_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Sequence of entity 6 (A, E), FASTA
>8X31_6 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS
Sequence of entity 7 (B, F), FASTA
>8X31_7 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG
Sequence of entity 8 (C, G), FASTA
>8X31_8 Histone H2A (chains C, G)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK
Sequence of entity 9 (D, H), FASTA
>8X31_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 P47128 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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
- 9VKW 3.13 Å, Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
- 9UUS 3.2 Å, The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail
- 5J9Q 3.25 Å, Crystal structure of the NuA4 core complex
- 7VVU 3.4 Å, NuA4 HAT module bound to the nucleosome
- 9UUO 3.68 Å, The NuA3 histone acetyltransferase complex
- 8X2X 3.8 Å, The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state
- 8X2Z 3.9 Å, The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
- 8X2Y 4.1 Å, The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
- 8X30 4.3 Å, Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex
Browse structure collections
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