8X2Z: The class2 of piccolo NuA4

The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state. Determined by electron microscopy at 3.9 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Saccharomyces cerevisiae, Escherichia coli, Schistosoma japonicum
Chains: 14
Atoms: 16,972
Mol. weight: 398.76 kDa
Released: 19 Mar 2025

Explore 8X2Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X2Z contains 62 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: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83	1	1
α-helix	86-113	28
α-helix	121-130	10

Chain B: 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	1	1
α-helix	83-92	10
β-strand	97	1	2

Chain C: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
α-helix	47-49	3
α-helix	50-61	12
α-helix	65-67	3
α-helix	70-73	4
β-strand	78-79	2	3
α-helix	81-86	6
α-helix	92-95	4
β-strand	101-103	3	4

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-50	10
β-strand	56-57	2	3
α-helix	61-86	26
α-helix	94-103	10
α-helix	107-126	20

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-73	10
β-strand	83	1	5
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	51-75	25
β-strand	80	1	5
α-helix	83-93	11
β-strand	96-98	3	4

Chain G: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	28-38	11
β-strand	43-44	2	6
α-helix	50-71	22
α-helix	72-74	3
β-strand	78-79	2	7
α-helix	82-88	7
β-strand	102	1	2

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	7
α-helix	59-86	28
β-strand	91-92	2	6
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	P47128
glutathione transferase,Enhancer of polycomb-like protein	M	protein	586	Schistosoma japonicum, Saccharomyces cerevisiae	P43572, Q540A3
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

>8X2Z_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS

Sequence of entity 2 (B, F), FASTA

>8X2Z_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG

Sequence of entity 3 (C, G), FASTA

>8X2Z_3 Histone H2A (chains C, G)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK

Sequence of entity 4 (D, H), FASTA

>8X2Z_4 Histone H2B (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA

Sequence of entity 5 (K), FASTA

>8X2Z_5 Histone acetyltransferase (chains K)
MGSSHHHHHHSQDHENLYFQGAGSMSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEER
LAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKK
KATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQ
NPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRK
KCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCM
TRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGS
PEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRY
YKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW

Sequence of entity 6 (L), FASTA

>8X2Z_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

>8X2Z_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

>8X2Z_8 Chromatin modification-related protein (chains N)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV

Sequence of entity 9 (I, J), FASTA

>8X2Z_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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