8X2X: The piccolo NuA4

The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state. Determined by electron microscopy at 3.8 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Escherichia coli, Saccharomyces cerevisiae, Schistosoma japonicum
Chains: 14
Atoms: 16,939
Mol. weight: 398.76 kDa
Released: 19 Mar 2025

Explore 8X2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X2X contains 60 α-helices and 27 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-76	13
β-strand	83-84	2	4
α-helix	86-113	28
β-strand	118	1	5
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	5
α-helix	50-75	26
β-strand	80-81	2	4
α-helix	83-93	11
β-strand	97-98	2	6

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	28-37	10
β-strand	43-44	2	7
α-helix	47-65	19
β-strand	78-79	2	8
α-helix	81-88	8
α-helix	93-97	5
β-strand	101-103	3	9

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-50	10
β-strand	56-57	2	8
α-helix	61-86	26
β-strand	91-92	2	7
α-helix	94-104	11
α-helix	107-125	19

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	10
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	50-75	26
β-strand	80-81	2	10
α-helix	83-93	11
β-strand	96-98	3	9

Chain G: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
β-strand	43-44	2	11
α-helix	50-71	22
α-helix	82-88	7
α-helix	92-95	4
β-strand	102-103	2	6

Chain H: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-51	11
α-helix	59-86	28
β-strand	91-92	2	11
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	P0AEX9 (AlphaFold model), 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, 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

>8X2X_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

>8X2X_2 Chromatin modification-related protein (chains N)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV

Sequence of entity 3 (K), FASTA

>8X2X_3 Histone acetyltransferase (chains K)
MGSSHHHHHHSQDHENLYFQGAGSMSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEER
LAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKK
KATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQ
NPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRK
KCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCM
TRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGS
PEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRY
YKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW

Sequence of entity 4 (M), FASTA

>8X2X_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

>8X2X_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 6 (A, E), FASTA

>8X2X_6 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS

Sequence of entity 7 (B, F), FASTA

>8X2X_7 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG

Sequence of entity 8 (C, G), FASTA

>8X2X_8 Histone H2A (chains C, G)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK

Sequence of entity 9 (D, H), FASTA

>8X2X_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 P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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