5J9W: NuA4 core complex
Crystal structure of the NuA4 core complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 26 Oct 2016.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 12
- Atoms
- 18,691
- Mol. weight
- 291.49 kDa
- Ligands
- ACO
- Released
- 26 Oct 2016
Explore 5J9W in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5J9W contains 123 α-helices and 63 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: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 161-163 | 3 | |
| β-strand | 169-172 | 4 | 8 |
| β-strand | 175-177 | 3 | 8 |
| α-helix | 187-191 | 5 | |
| β-strand | 194-197 | 4 | 8 |
| β-strand | 204-205 | 2 | 8 |
| α-helix | 208-217 | 10 | |
| β-strand | 226-230 | 5 | 9 |
| β-strand | 235-240 | 6 | 9 |
| α-helix | 245-256 | 12 | |
| β-strand | 266 | 1 | 10 |
| β-strand | 271-279 | 9 | 9 |
| β-strand | 284-293 | 10 | 9 |
| β-strand | 300-302 | 3 | 11 |
| β-strand | 305-307 | 3 | 9 |
| α-helix | 309-311 | 3 | |
| α-helix | 316-330 | 15 | |
| β-strand | 335 | 1 | 12 |
| β-strand | 336-337 | 2 | 11 |
| α-helix | 343-364 | 22 | |
| α-helix | 370-377 | 8 | |
| β-strand | 379 | 1 | 12 |
| α-helix | 381-390 | 10 | |
| β-strand | 394-397 | 4 | 13 |
| β-strand | 400-403 | 4 | 13 |
| α-helix | 407-419 | 13 | |
| α-helix | 426-428 | 3 | |
| β-strand | 429 | 1 | 9 |
Chain B: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 6-43 | 38 | |
| α-helix | 90-92 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 100-106 | 7 | |
Chain C: 21 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 129 | 1 | 8 |
| 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 | 232-243 | 12 | |
| α-helix | 256-260 | 5 | |
| α-helix | 261-263 | 3 | |
| α-helix | 264-270 | 7 | |
| α-helix | 272-285 | 14 | |
| β-strand | 296 | 1 | 14 |
| α-helix | 303-304 | 2 | |
| β-strand | 310 | 1 | 14 |
| β-strand | 313 | 1 | 10 |
| α-helix | 319-323 | 5 | |
| α-helix | 324-382 | 59 | |
Chains D, H and L: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 17-56 | 40 | |
| α-helix | 61-62 | 2 | |
| α-helix | 65-112 | 48 | |
Chains E and I: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 161-163 | 3 | |
| β-strand | 169-172 | 4 | 1 |
| β-strand | 175-177 | 3 | 1 |
| α-helix | 187-191 | 5 | |
| β-strand | 194-197 | 4 | 1 |
| β-strand | 204-205 | 2 | 1 |
| α-helix | 208-217 | 10 | |
| β-strand | 226-230 | 5 | 2 |
| β-strand | 235-240 | 6 | 2 |
| α-helix | 245-256 | 12 | |
| β-strand | 266 | 1 | 3 |
| β-strand | 271-279 | 9 | 2 |
| β-strand | 284-293 | 10 | 2 |
| β-strand | 300-302 | 3 | 4 |
| β-strand | 305-307 | 3 | 2 |
| α-helix | 309-311 | 3 | |
| α-helix | 316-330 | 15 | |
| β-strand | 335 | 1 | 5 |
| β-strand | 336-337 | 2 | 4 |
| α-helix | 343-364 | 22 | |
| α-helix | 370-377 | 8 | |
| β-strand | 379 | 1 | 5 |
| α-helix | 381-390 | 10 | |
| β-strand | 394-397 | 4 | 6 |
| β-strand | 400-403 | 4 | 6 |
| α-helix | 407-418 | 12 | |
| α-helix | 426-428 | 3 | |
| β-strand | 429 | 1 | 2 |
Chain F: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-43 | 36 | |
| α-helix | 90-92 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 100-106 | 7 | |
Chain G: 23 helices, 4 β-strands
| 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 | 256-260 | 5 | |
| α-helix | 261-263 | 3 | |
| α-helix | 264-267 | 4 | |
| α-helix | 268-272 | 5 | |
| α-helix | 273-285 | 13 | |
| β-strand | 296 | 1 | 7 |
| α-helix | 303-304 | 2 | |
| β-strand | 310 | 1 | 7 |
| β-strand | 313 | 1 | 3 |
| α-helix | 319-323 | 5 | |
| α-helix | 324-382 | 59 | |
| α-helix | 388-391 | 4 | |
Chain J: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-43 | 37 | |
| α-helix | 90-92 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 100-106 | 7 | |
1 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 acetyltransferase ESA1 | A, E, I | protein | 305 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q08649 (AlphaFold model) |
| Chromatin modification-related protein EAF6 | B, F, J | protein | 113 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P47128 (AlphaFold model) |
| Enhancer of polycomb-like protein 1 | C, G, K | protein | 280 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P43572 (AlphaFold model) |
| Chromatin modification-related protein YNG2 | D, H, L | protein | 120 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38806 (AlphaFold model) |
Sequence of entity 1 (A, E, I), FASTA
>5J9W_1 Histone acetyltransferase ESA1 (chains A, E, I)
HEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDF
TLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLD
HKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLL
IEFSYELSKKENKVGSPQKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMT
TTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQ
LRFAW
Sequence of entity 2 (B, F, J), FASTA
>5J9W_2 Chromatin modification-related protein EAF6 (chains B, F, J)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND
Sequence of entity 3 (C, G, K), FASTA
>5J9W_3 Enhancer of polycomb-like protein 1 (chains C, G, K)
IPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGS
SDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNH
EINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERP
GEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLN
WINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT
Sequence of entity 4 (D, H, L), FASTA
>5J9W_4 Chromatin modification-related protein YNG2 (chains D, H, L)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ACO | Acetyl coenzyme *a | C23 H38 N7 O17 P3 S | 2 |
Primary citation
The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism. Xu, P., Li, C., Chen, Z. et al. Mol Cell (2016) 63:965-975. DOI 10.1016/j.molcel.2016.07.024 · PubMed
Other PDB entries of the same protein (UniProt Q08649 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TO7 1.9 Å, Crystal structure of yeast Esa1 HAT domain bound to coenzyme A with active site lysine…
- 1FY7 2.0 Å, Crystal structure of yeast ESA1 histone acetyltransferase domain complexed with coenzyme a
- 3TO9 2.0 Å, Crystal structure of yeast Esa1 E338Q HAT domain bound to coenzyme A with active site…
- 3TO6 2.1 Å, Crystal structure of yeast Esa1 HAT domain complexed with H4K16CoA bisubstrate inhibitor
- 1MJA 2.26 Å, Crystal structure of yeast Esa1 histone acetyltransferase domain complexed with acetyl…
- 1MJ9 2.5 Å, Crystal structure of yeast Esa1(C304S) mutant complexed with Coenzyme A
- 1MJB 2.5 Å, Crystal structure of yeast Esa1 histone acetyltransferase E338Q mutant complexed with…
- 5J9T 2.7 Å, Crystal structure of the NuA4 core complex
- 5J9U 2.95 Å, Crystal structure of the NuA4 core complex
- 5J9Q 3.25 Å, Crystal structure of the NuA4 core complex
- 7VVU 3.4 Å, NuA4 HAT module bound to the nucleosome
- 8X2X 3.8 Å, The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state
Browse structure collections
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