7VVZ: NuA4

NuA4 bound to the nucleosome. Determined by electron microscopy at 8.8 Å resolution. Released 10 Aug 2022.

Method: Electron microscopy
Resolution: 8.8 Å
Organisms: Saccharomyces cerevisiae S288C, Xenopus laevis, Saccharomyces cerevisiae
Chains: 21
Atoms: 61,920
Mol. weight: 1251.79 kDa
Ligands: CMC, MG, ATP
Released: 10 Aug 2022

Explore 7VVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VVZ contains 373 α-helices and 123 β-strands across 18 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.

Chains A and O: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	9
α-helix	121-131	11

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	9
α-helix	50-75	26
β-strand	80-81	2	8
α-helix	83-92	10
β-strand	96-98	3	7

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	11
α-helix	56-83	28
β-strand	88-89	2	10
α-helix	91-101	11
α-helix	104-123	20

Chain E: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	226-228	3
α-helix	242-247	6
β-strand	268-273	6	16
β-strand	280-282	3	17
α-helix	287-294	8
α-helix	299-301	3
α-helix	313-336	24
β-strand	345	1	18
α-helix	346-348	3
α-helix	358-396	39
β-strand	546-548	3	19
α-helix	549-551	3
α-helix	554-562	9
β-strand	566	1	19
β-strand	598	1	19
β-strand	599-604	6	16
α-helix	613-616	4
α-helix	628-630	3
α-helix	636-638	3
α-helix	654-665	12
α-helix	671-676	6
α-helix	693-703	11
α-helix	717-734	18
β-strand	742-743	2	20
α-helix	745-747	3
α-helix	750-752	3
α-helix	757-771	15
α-helix	797-806	10

Chain F: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	21
β-strand	25-30	6	21
β-strand	38-41	4	21
β-strand	43-44	2	22
β-strand	45-46	2	23
β-strand	55-56	2	23
β-strand	72-73	2	22
β-strand	75-76	2	24
β-strand	79-80	2	24
α-helix	83-97	15
β-strand	108-112	5	21
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-141	6	21
α-helix	142-150	9
β-strand	155-160	6	25
β-strand	165-171	7	25
β-strand	174-175	2	25
α-helix	177-179	3
β-strand	181-183	3	25
α-helix	187-197	11
α-helix	206-208	3
β-strand	209-211	3	26
β-strand	217-218	2	26
α-helix	224-226	3
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-246	7
α-helix	258-263	6
α-helix	266-267	2
β-strand	268-271	4	27
β-strand	277-280	4	27
α-helix	282-290	9
α-helix	385-394	10
α-helix	401-406	6
β-strand	408-411	4	25
α-helix	414-416	3
α-helix	420-431	12
α-helix	445-449	5
α-helix	451-460	10
α-helix	466-468	3
β-strand	470-471	2	21
α-helix	472-478	7

Chain G: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	28
β-strand	16-21	6	28
β-strand	29-32	4	28
β-strand	35-36	2	29
β-strand	53-54	2	29
α-helix	56-60	5
β-strand	68	1	29
β-strand	71-72	2	30
β-strand	75-76	2	30
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	28
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	28
α-helix	137-144	8
β-strand	150-155	6	31
β-strand	160-166	7	31
β-strand	169-170	2	31
α-helix	172-174	3
β-strand	176-178	3	31
α-helix	182-193	12
α-helix	194-196	3
α-helix	206-216	11
α-helix	223-232	10
β-strand	238-241	4	32
β-strand	247-250	4	32
α-helix	256-259	4
α-helix	274-283	10
α-helix	291-294	4
β-strand	297-300	4	31
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	31
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	28
α-helix	359-365	7
α-helix	369-373	5

Chain H: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	489-490	2	20
α-helix	493-495	3
α-helix	505-530	26
β-strand	535	1	18
β-strand	546-549	4	34
α-helix	560-562	3
α-helix	564-567	4
β-strand	572-576	5	34
α-helix	581-586	6
β-strand	593-595	3	16
β-strand	601	1	16
α-helix	611-615	5
α-helix	617	1
β-strand	618-620	3	17
β-strand	632-633	2	16
α-helix	634	1
β-strand	636-642	7	19
β-strand	648-654	7	19
α-helix	667-670	4
α-helix	673-680	8
β-strand	692-693	2	27
α-helix	694-696	3
α-helix	698-710	13
α-helix	714-716	3
α-helix	725-730	6
α-helix	735-765	31

Chain K: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	43-49	7
β-strand	57-60	4	19
α-helix	75-77	3
β-strand	78-84	7	33
β-strand	90-96	7	33
β-strand	108	1	33
α-helix	110-114	5
α-helix	125-131	7
α-helix	166-178	13
α-helix	183-189	7
α-helix	199-215	17
α-helix	221-224	4
α-helix	230-244	15
α-helix	248-265	18
α-helix	268-282	15
α-helix	291-295	5
α-helix	297-308	12
α-helix	322-324	3
α-helix	325-328	4

8 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
Chromatin modification-related protein EAF6	Y	protein	113	Saccharomyces cerevisiae S288C	P47128 (AlphaFold model)
Chromatin modification-related protein YNG2	V	protein	282	Saccharomyces cerevisiae S288C	P38806 (AlphaFold model)
Enhancer of polycomb-like protein 1	H, T	protein	832	Saccharomyces cerevisiae S288C	P43572 (AlphaFold model)
Histone H3	A, O	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, Q	protein	103	Xenopus laevis	P62799
Histone H2A	N, S	protein	130	Xenopus laevis	P06897
Histone H2B 1.1	D, U	protein	126	Xenopus laevis	P02281
Histone acetyltransferase ESA1	P	protein	445	Saccharomyces cerevisiae S288C	Q08649
DNA (207-mer)	W	DNA	207	Saccharomyces cerevisiae
DNA (207-mer)	I	DNA	207	Saccharomyces cerevisiae
Epl1 arginine anchor	X	protein	9	Saccharomyces cerevisiae	P43572 (AlphaFold model)
Chromatin modification-related protein EAF1	E	protein	1168	Saccharomyces cerevisiae S288C	Q06337

4 more molecules are not listed.

Sequence of entity 1 (Y), FASTA

>7VVZ_1 Chromatin modification-related protein EAF6 (chains Y)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Sequence of entity 2 (V), FASTA

>7VVZ_2 Chromatin modification-related protein YNG2 (chains V)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
EEDGDMDSAAEASRESSVVSNSSVKKRRAASSSGSVPPTLKKKKTSRTSKLQNEIDVSSR
EKSVTPVSPSIEKKIARTKEFKNSRNGKGQNGSPENEEEDKTLYCFCQRVSFGEMVACDG
PNCKYEWFHYDCVNLKEPPKGTWYCPECKIEMEKNKLKRKRN

Sequence of entity 3 (H, T), FASTA

>7VVZ_3 Enhancer of polycomb-like protein 1 (chains H, T)
MPTPSNAIEINDGSHKSGRSTRRSGSRSAHDDGLDSFSKGDSGAGASAGSSNSRFRHRKI
SVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGHTKHKDY
IPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGS
SDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNH
EINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERP
GEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLN
WINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPTIVTVEQREAELRKAELKRAA
AAAAAAKAKNNKRNNQLEDKSSRLTKQQQQQLLQQQQQQQQNALKTENGKQLANASSSST
SQPITSHVYVKLPSSKIPDIVLEDVDALLNSKEKNARKFVQEKMEKRKIEDADVFFNLTD
DPFNPVFDMSLPKNFSTSNVPFASIASSKFQIDRSFYSSHLPEYLKGISDDIRIYDSNGR
SRNKDNYNLDTKRIKKTELYDPFQENLEIHSREYPIKFRKRVGRSNIKYVDRMPNFTTSS
TKSACSLMDFVDFDSIEKEQYSREGSNDTDSINVYDSKYDEFVRLYDKWKYDSPQNEYGI
KFSDEPARLNQISNDTQVIRFGTMLGTKSYEQLREATIKYRRDYITRLKQKHIQHLQQQQ
QQQQQQQQQAQQQKQKSQNNNSNSSNSLKKLNDSLINSEAKQNSSITQKNSS

Sequence of entity 4 (A, O), FASTA

>7VVZ_4 Histone H3 (chains A, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (B, Q), FASTA

>7VVZ_5 Histone H4 (chains B, Q)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (N, S), FASTA

>7VVZ_6 Histone H2A (chains N, S)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 7 (D, U), FASTA

>7VVZ_7 Histone H2B 1.1 (chains D, U)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 8 (P), FASTA

>7VVZ_8 Histone acetyltransferase ESA1 (chains P)
MSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEERLAEILSINTRKAPPKFYVHYVNYN
KRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKKKATNTSETPQDSLQDGVDGFSREN
TDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPW
YFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEID
GRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGY
NVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITL
LVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKK
RRTIDPNRLIWKPPVFTASQLRFAW

Sequence of entity 9 (W), FASTA

>7VVZ_9 DNA (207-mer) (chains W)
TCCGGAGGACTGTCCTCCGGGGACCCTATACGCGGCCGCCATCGAGAATCCCGGTGCCGA
GGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCGATAGCTTGTCGAGAAGTACTAG

Sequence of entity 10 (I), FASTA

>7VVZ_10 DNA (207-mer) (chains I)
CTAGTACTTCTCGACAAGCTATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATGGCGGCCGCGTAT
AGGGTCCCCGGAGGACAGTCCTCCGGA

Sequence of entity 11 (X), FASTA

>7VVZ_11 Epl1 arginine anchor (chains X)
FRHRKISVK

Sequence of entity 12 (E), FASTA

>7VVZ_12 Chromatin modification-related protein EAF1 (chains E)
MSSRPSSAVPNSASLSEDQSSDRSKFPKADDLIDERDRKLTELYCVSRLNQLLELTDENK
LRKEIDAFLKKNDIRRGIRFDEASLPKLLHTAATPITKKKLKDVNLINVPNQRLSDSKMS
RELPENSENVSVKSESHFVPSHDNSIRENMMDSLRPAEKTGGMWNKRPLESTMGGEEERH
EKRQKMQSQSLESSNNSEMASLPISPRPPVPNALAHYTYYENIEYPPADPTEVQPAVKFK
DPLIKNIMAKEIDTSDHYNENNVDALETVFLLMNDYIPSKIPQALPLAELKYMSQTLPLI
NLIPRAHKALTTNIINNALNEARITVVGSRIEELRRLGLWSLRQPKRFIDPWKQHNTHQN
ILLEEAKWMQADFKEGHKYKVAICTAMAQAIKDYWTYGEICCVKRKTLLPGKENKLSDDG
RISEKSGRPSDTSRNDSDISIAGKDDIGIIANVDDITEKESAAANDNDENGKNEAGAKSD
FDFADGLLSQEGAHDQIISSIDTKLLLKKPSSSSEVVLIQHEVAASSALIETEESKKELA
PPFKLSIFVDELNTFEKTLIQDLPLYNGINEERPKKDDSLPFIPISKSVVSLDDNGFYKL
LERQLIDEEPSISQLSKRRGMFYGNRRNHYLRPPAVPSLRYLQNRTPTIWLSEDDQELVK
NINTYGYNWELISAHMTHRLTYSYLSNIERRTPWQCFERFVQLNERFNFSDLKGPRAHSA
QQWLIEAHKFQQRQNRRISPLGVNTESIQRGHRRLRWASMFEAIRKCMKKRENTPRPNPT
QPRKPLDCKNMKVPTPAEMSLLKAQRDEALRRDIQLRRTVKNRLQQRQQQSQQAHSSRAQ
SPIPSNGKSSSNLARNGQASAPRPNQKQYTEQDIIESYSRKLLEQKPDIGPEMALKAAKN
YYRTLREQQQQLKQHQIQQQRQQLQEESSHVQQLQQLQPGSQAPPPKSSPSQSSLSNISN
INSAPRIKSPTPQEILQRFQKQRTLQVDWSHPQFEKHHHHHHHHHHHHDYDIPTTASVDG
SENLYFQGSPQQNKTAALAQHDEAVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKD
DPSQSANLLAEAKKLNDAQAPKVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDP
SQSANLLAEAKKLNDAQAPKVDANSAAL

Ligands and cofactors

ID	Name	Formula	Copies
CMC	Carboxymethyl coenzyme *a	C23 H38 N7 O18 P3 S	1
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structure of the NuA4 acetyltransferase complex bound to the nucleosome. Qu, K., Chen, K., Wang, H. et al. Nature (2022) 610:569-574. DOI 10.1038/s41586-022-05303-x · 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

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