5J9U: NuA4 core complex

Crystal structure of the NuA4 core complex. Determined by X-ray diffraction at 2.95 Å resolution. Released 26 Oct 2016.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 12
Atoms: 19,676
Mol. weight: 315.41 kDa
Released: 26 Oct 2016

Explore 5J9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J9U contains 115 α-helices and 80 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	161	1	13
β-strand	170-172	3	14
β-strand	175-177	3	14
α-helix	187-190	4
β-strand	195-197	3	14
β-strand	204-205	2	14
α-helix	208-217	10
β-strand	226-230	5	15
β-strand	235-240	6	15
α-helix	245-256	12
β-strand	266	1	16
β-strand	271-279	9	15
β-strand	284-293	10	15
β-strand	300-302	3	17
β-strand	305-307	3	15
α-helix	309-311	3
α-helix	316-331	16
β-strand	335	1	18
β-strand	336-337	2	17
α-helix	343-364	22
β-strand	368	1	10
α-helix	370-377	8
β-strand	379	1	18
α-helix	381-390	10
β-strand	394-396	3	9
β-strand	401-404	4	9
α-helix	407-418	12
α-helix	426-428	3
β-strand	429	1	15
α-helix	432-434	3
β-strand	437	1	1

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-43	42
α-helix	90-92	3
α-helix	96-98	3
α-helix	100-105	6

Chain C: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	65-67	3	24
β-strand	73-75	3	27
β-strand	121-123	3	27
α-helix	124-127	4
β-strand	128-129	2	14
α-helix	133-136	4
α-helix	142-144	3
α-helix	147-148	2
α-helix	154-157	4
α-helix	166-171	6
α-helix	172-176	5
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	232-241	10
α-helix	256-258	3
α-helix	264-267	4
α-helix	268-272	5
α-helix	273-285	13
β-strand	296-297	2	28
α-helix	298-299	2
β-strand	310-311	2	28
β-strand	313	1	16
α-helix	328-382	55
α-helix	389-391	3

Chains D and K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-13	11
α-helix	17-56	40
α-helix	61-62	2
α-helix	65-113	49
α-helix	118-119	2

Chain E: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	161	1	1
β-strand	170-172	3	2
β-strand	175-177	3	2
α-helix	187-190	4
β-strand	195-197	3	2
β-strand	204-205	2	2
α-helix	208-217	10
β-strand	226-230	5	3
β-strand	235-240	6	3
α-helix	245-256	12
β-strand	266	1	4
β-strand	271-279	9	3
β-strand	284-293	10	3
β-strand	300-302	3	5
β-strand	305-307	3	3
α-helix	309-311	3
α-helix	316-331	16
β-strand	335	1	6
β-strand	336-337	2	5
α-helix	343-364	22
α-helix	370-377	8
β-strand	379	1	6
α-helix	381-390	10
β-strand	394-396	3	7
β-strand	401-403	3	7
α-helix	407-418	12
α-helix	426-428	3
β-strand	429	1	3
α-helix	432-435	4
β-strand	437	1	8

Chains F and J: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-43	42
α-helix	90-92	3
α-helix	96-98	3

Chain G: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	65-67	3	9
β-strand	68	1	10
β-strand	73-75	3	11
β-strand	121-123	3	11
α-helix	124-127	4
β-strand	128-129	2	2
α-helix	130	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	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	232-241	10
α-helix	256-260	5
α-helix	264-267	4
α-helix	268-272	5
α-helix	273-285	13
β-strand	296-297	2	12
α-helix	298-299	2
β-strand	310-311	2	12
β-strand	313	1	4
α-helix	328-382	55

Chain H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-13	11
α-helix	17-56	40
α-helix	61-62	2
α-helix	65-113	49

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
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, N	protein	351	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P43572 (AlphaFold model)
Chromatin modification-related protein YNG2	D, H, K	protein	120	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38806 (AlphaFold model)

Sequence of entity 1 (A, E, I), FASTA

>5J9U_1 Histone acetyltransferase ESA1 (chains A, E, I)
HEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDF
TLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLD
HKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLL
IEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMT
TTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQ
LRFAW

Sequence of entity 2 (B, F, J), FASTA

>5J9U_2 Chromatin modification-related protein EAF6 (chains B, F, J)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Sequence of entity 3 (C, G, N), FASTA

>5J9U_3 Enhancer of polycomb-like protein 1 (chains C, G, N)
SSNSRFRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQ
MGSGHTKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDE
TFLNEQVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDM
ADFNLRNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGY
EIFPQLKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLAL
LVAKRENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT

Sequence of entity 4 (D, H, K), FASTA

>5J9U_4 Chromatin modification-related protein YNG2 (chains D, H, K)
MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIP
KHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV

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
5J9W 2.8 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

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