SMTL ID : 7vvz.1

NuA4 bound to the nucleosome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-2-2-2-1-1-1-1-1-1-mer

Ligands

1 x PHE- ARG- HIS- ARG- LYS- ILE- SER- VAL- LYS: Epl1 arginine anchor(Non-covalent)

PHE-ARG-HIS-ARG-LYS-ILE-SER-VAL-LYS.1: 13 residues within 4Å: Chain J: Y.58, E.62, E.65, D.91, E.93 Chain K: E.106, L.107, H.110, E.114 Chain L: T.369, D.371, K.389, H.401 8 PLIP interactions: 5 interactions with chain J, 2 interactions with chain L, 1 interactions with chain K Hydrogen bonds: J:E.62, J:E.62, L:K.389, L:K.389 Salt bridges: J:E.62, J:D.91, J:E.93, K:E.114

1 x CMC: CARBOXYMETHYL COENZYME *A(Covalent)

CMC.2: 21 residues within 4Å: Chain I: K.17 Chain L: F.258, L.259, A.303, C.304, I.305, L.306, T.307, Q.312, R.313, M.314, G.315, Y.316, G.317, K.318, E.338, P.340, L.344, L.347, A.351, R.421 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:L.259, L:L.344 Hydrogen bonds: L:T.307, L:T.307, L:T.307, L:Y.311, L:Q.312, L:R.313, L:M.314, L:G.315, L:Y.316, L:G.317, L:K.318 Salt bridges: L:R.421

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain P: D.159 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain Q: Q.137 Ligands: ATP.6 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 18 residues within 4Å: Chain P: G.22, S.23, Y.24, T.25, G.161, H.162, D.163, T.164, G.187, Q.240, K.243, E.244, G.412, G.413, T.414, I.417, Q.449 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain P Hydrogen bonds: P:S.23, P:Y.24, P:Y.24, P:T.25, P:H.162, P:H.162, P:D.163, P:T.164, P:Q.240, P:K.243, P:G.413, P:T.414 ATP.6: 20 residues within 4Å: Chain Q: G.13, S.14, G.15, M.16, K.18, D.154, S.155, G.156, D.157, V.159, G.182, K.213, E.214, G.301, G.302, T.303, M.305, F.306, K.336 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain Q Hydrogen bonds: Q:S.14, Q:G.15, Q:M.16, Q:M.16, Q:Q.137, Q:D.154, Q:D.157, Q:D.157, Q:K.213, Q:G.302, Q:T.303, Q:M.305, Q:K.336 Salt bridges: Q:K.18, Q:K.18 pi-Stacking: Q:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qu, K. et al., Structure of the NuA4 acetyltransferase complex bound to the nucleosome. Nature (2022)

Release Date

2022-08-10

Peptides

Chromatin modification-related protein EAF6: A
Chromatin modification-related protein YNG2: B
Enhancer of polycomb-like protein 1: CS
Histone H3: DH
Histone H4: EI
Histone H2A: FJ
Histone H2B 1.1: GK
Histone acetyltransferase ESA1: L
Chromatin modification-related protein EAF1: O
Actin-related protein 4: P
Actin: Q
SWR1-complex protein 4: R
Transcription-associated protein 1: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
V

C
T

S
H

D
O

H
A

E
Q

I
B

F
S

J
N

G
U

K
D

L
P

O
E

P
F

Q
G

R
K

T
L

Chromatin modification-related protein EAF6

Chromatin modification-related protein YNG2

Enhancer of polycomb-like protein 1

Histone H3

Histone H4

Histone H2A

Histone H2B 1.1

Histone acetyltransferase ESA1

Chromatin modification-related protein EAF1

Actin-related protein 4

Actin

SWR1-complex protein 4

Transcription-associated protein 1

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