7VVU: NuA4 HAT module
NuA4 HAT module bound to the nucleosome. Determined by electron microscopy at 3.4 Å resolution. Released 10 Aug 2022.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Saccharomyces cerevisiae, Xenopus laevis
- Chains
- 15
- Atoms
- 19,374
- Mol. weight
- 529.99 kDa
- Ligands
- CMC
- Released
- 10 Aug 2022
Explore 7VVU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VVU contains 77 α-helices and 37 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.
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 | |
Chains N and S: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 11 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 4 |
| α-helix | 113-115 | 3 | |
Chain P: 10 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 170-172 | 3 | 1 |
| β-strand | 175-177 | 3 | 1 |
| α-helix | 187-190 | 4 | |
| β-strand | 195-197 | 3 | 1 |
| β-strand | 204-205 | 2 | 1 |
| α-helix | 208-217 | 10 | |
| β-strand | 226-230 | 5 | 12 |
| β-strand | 234-240 | 7 | 12 |
| α-helix | 245-256 | 12 | |
| β-strand | 271-279 | 9 | 12 |
| β-strand | 284-293 | 10 | 12 |
| β-strand | 300-302 | 3 | 13 |
| β-strand | 305-307 | 3 | 12 |
| α-helix | 309-311 | 3 | |
| α-helix | 316-330 | 15 | |
| β-strand | 335 | 1 | 14 |
| β-strand | 336-337 | 2 | 13 |
| α-helix | 343-364 | 22 | |
| α-helix | 370-377 | 8 | |
| β-strand | 379 | 1 | 14 |
| α-helix | 381-390 | 10 | |
| β-strand | 394-396 | 3 | 15 |
| β-strand | 401-403 | 3 | 15 |
| α-helix | 407-419 | 13 | |
| α-helix | 426-428 | 3 | |
| β-strand | 429 | 1 | 12 |
Chain Q: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 3 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 4 |
Chain T: 22 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 128-129 | 2 | 1 |
| α-helix | 133-136 | 4 | |
| α-helix | 142-144 | 3 | |
| α-helix | 147-148 | 2 | |
| α-helix | 155-157 | 3 | |
| α-helix | 166-171 | 6 | |
| α-helix | 172-176 | 5 | |
| α-helix | 183-185 | 3 | |
| α-helix | 186-203 | 18 | |
| α-helix | 207-209 | 3 | |
| α-helix | 211-213 | 3 | |
| α-helix | 214-216 | 3 | |
| α-helix | 217-226 | 10 | |
| α-helix | 229-231 | 3 | |
| α-helix | 232-241 | 10 | |
| α-helix | 256-259 | 4 | |
| α-helix | 262-263 | 2 | |
| α-helix | 264-285 | 22 | |
| α-helix | 314-316 | 3 | |
| α-helix | 328-329 | 2 | |
| α-helix | 330-334 | 5 | |
| α-helix | 335-382 | 48 | |
| α-helix | 389-391 | 3 | |
Chain U: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 6 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
2 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 | P47128 (AlphaFold model) |
| Chromatin modification-related protein YNG2 | V | protein | 282 | Saccharomyces cerevisiae | P38806 (AlphaFold model) |
| Enhancer of polycomb-like protein 1 | T, X | protein | 832 | Saccharomyces cerevisiae | P43572 (AlphaFold model) |
| Histone H3 | A, O | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| 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 | Q08649 |
| DNA (207-mer) | W | DNA | 207 | Saccharomyces cerevisiae | |
| DNA (207-mer) | I | DNA | 207 | Saccharomyces cerevisiae | |
Sequence of entity 1 (Y), FASTA
>7VVU_1 Chromatin modification-related protein EAF6 (chains Y)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND
Sequence of entity 2 (V), FASTA
>7VVU_2 Chromatin modification-related protein YNG2 (chains V)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
EEDGDMDSAAEASRESSVVSNSSVKKRRAASSSGSVPPTLKKKKTSRTSKLQNEIDVSSR
EKSVTPVSPSIEKKIARTKEFKNSRNGKGQNGSPENEEEDKTLYCFCQRVSFGEMVACDG
PNCKYEWFHYDCVNLKEPPKGTWYCPECKIEMEKNKLKRKRN
Sequence of entity 3 (T, X), FASTA
>7VVU_3 Enhancer of polycomb-like protein 1 (chains T, X)
MPTPSNAIEINDGSHKSGRSTRRSGSRSAHDDGLDSFSKGDSGAGASAGSSNSRFRHRKI
SVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGHTKHKDY
IPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGS
SDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNH
EINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERP
GEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLN
WINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPTIVTVEQREAELRKAELKRAA
AAAAAAKAKNNKRNNQLEDKSSRLTKQQQQQLLQQQQQQQQNALKTENGKQLANASSSST
SQPITSHVYVKLPSSKIPDIVLEDVDALLNSKEKNARKFVQEKMEKRKIEDADVFFNLTD
DPFNPVFDMSLPKNFSTSNVPFASIASSKFQIDRSFYSSHLPEYLKGISDDIRIYDSNGR
SRNKDNYNLDTKRIKKTELYDPFQENLEIHSREYPIKFRKRVGRSNIKYVDRMPNFTTSS
TKSACSLMDFVDFDSIEKEQYSREGSNDTDSINVYDSKYDEFVRLYDKWKYDSPQNEYGI
KFSDEPARLNQISNDTQVIRFGTMLGTKSYEQLREATIKYRRDYITRLKQKHIQHLQQQQ
QQQQQQQQQAQQQKQKSQNNNSNSSNSLKKLNDSLINSEAKQNSSITQKNSS
Sequence of entity 4 (A, O), FASTA
>7VVU_4 Histone H3 (chains A, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 5 (B, Q), FASTA
>7VVU_5 H4 (chains B, Q)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 6 (N, S), FASTA
>7VVU_6 Histone H2A (chains N, S)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 7 (D, U), FASTA
>7VVU_7 Histone H2B 1.1 (chains D, U)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 8 (P), FASTA
>7VVU_8 Histone acetyltransferase ESA1 (chains P)
MSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEERLAEILSINTRKAPPKFYVHYVNYN
KRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKKKATNTSETPQDSLQDGVDGFSREN
TDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPW
YFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEID
GRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGY
NVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITL
LVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKK
RRTIDPNRLIWKPPVFTASQLRFAW
Sequence of entity 9 (W), FASTA
>7VVU_9 DNA (207-mer) (chains W)
TCCGGAGGACTGTCCTCCGGGGACCCTATACGCGGCCGCCATCGAGAATCCCGGTGCCGA
GGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCGATAGCTTGTCGAGAAGTACTAG
Sequence of entity 10 (I), FASTA
>7VVU_10 DNA (207-mer) (chains I)
CTAGTACTTCTCGACAAGCTATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATGGCGGCCGCGTAT
AGGGTCCCCGGAGGACAGTCCTCCGGA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CMC | Carboxymethyl coenzyme *a | C23 H38 N7 O18 P3 S | 1 |
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
- 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
- 8X32 4.4 Å, The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state
Browse structure collections
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