SMTL ID : 8xvt.1

The core subcomplex of human NuA4/TIP60 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-2-1-1-1-mer

Ligands

9 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)(Covalent)

ADP.1: 21 residues within 4Å: Chain A: S.17, H.18, H.20, G.38, L.39, V.40, G.41, P.72, G.73, T.74, G.75, K.76, T.77, A.78, N.332, Y.366, I.374, R.404 Chain B: R.314, E.317, R.353 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.17, A:S.17, A:V.40, A:G.41, A:G.73, A:T.74, A:T.74, A:G.75, A:K.76, A:T.77, A:T.77, A:A.78, A:N.332, A:Y.366, A:R.378, A:R.404, A:R.404 Salt bridges: A:H.18, A:K.76, B:R.314, B:R.314, B:R.353, B:R.353 ADP.2: 22 residues within 4Å: Chain B: A.24, H.25, H.27, G.45, M.46, V.47, G.48, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, I.370, R.374, L.399, R.400 Chain C: E.320, R.357 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.25, B:V.47, B:G.48, B:G.80, B:G.82, B:K.83, B:T.84, B:T.84, B:T.84, B:T.84, B:A.85, B:N.329, B:N.329, B:Y.362, B:Y.362, B:R.374 Salt bridges: B:H.25, B:K.83, B:R.400, B:R.400, C:R.357 ADP.3: 16 residues within 4Å: Chain C: S.17, H.18, H.20, G.38, L.39, V.40, P.71, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.17, C:S.17, C:V.40, C:G.41, C:G.73, C:T.74, C:G.75, C:K.76, C:T.77, C:T.77, C:A.78, C:Y.366 Salt bridges: C:H.18, C:K.76 ADP.4: 16 residues within 4Å: Chain D: A.24, H.25, H.27, V.47, Q.78, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.24, D:Q.78, D:G.80, D:T.81, D:G.82, D:K.83, D:T.84, D:T.84, D:T.84, D:A.85, D:Y.362, D:Y.362, D:R.400, E:R.357 Salt bridges: D:H.25, D:K.83, D:R.400 ADP.5: 17 residues within 4Å: Chain E: S.17, H.18, H.20, G.38, L.39, V.40, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.378, R.404 Chain F: R.353 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:S.17, E:H.20, E:V.40, E:G.73, E:T.74, E:G.75, E:K.76, E:T.77, E:T.77, E:A.78, E:Y.366, E:Y.366, F:R.353, F:R.353 Salt bridges: E:H.18, E:K.76, E:R.404, E:R.404, F:R.353 ADP.6: 22 residues within 4Å: Chain A: E.320 Chain F: A.24, H.25, H.27, G.45, M.46, V.47, G.48, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, R.374, L.399, R.400, I.403 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:A.24, F:V.47, F:G.80, F:T.81, F:G.82, F:K.83, F:T.84, F:T.84, F:T.84, F:A.85, F:N.329, F:Y.362, A:E.320 Salt bridges: F:H.25, F:K.83, F:R.400, F:R.400 ADP.7: 16 residues within 4Å: Chain I: S.20, Y.21, T.22, R.24, D.171, G.173, A.174, T.175, H.176, Q.260, Q.263, A.264, G.353, N.354, L.356, R.390 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:S.20, I:S.20, I:Y.21, I:T.22, I:A.174, I:Q.263, I:A.264, I:G.353, I:R.390 ADP.8: 16 residues within 4Å: Chain J: S.20, Y.21, T.22, R.24, G.91, D.171, G.173, A.174, H.176, Q.260, A.264, G.353, N.354, L.356, I.357, R.390 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.20, J:Y.21, J:T.22, J:T.22, J:R.24, J:R.24, J:A.174, J:G.353, J:N.354, J:R.390 ADP.9: 16 residues within 4Å: Chain K: D.11, G.13, S.14, M.16, K.18, D.154, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, K.336 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:D.11, K:S.14, K:D.157, K:D.157, K:R.210, K:K.213, K:G.302, K:T.303 Salt bridges: K:K.18, K:K.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, K. et al., Structure of the human TIP60 complex. Nat Commun (2024)

Release Date

2024-07-24

Peptides

RuvB-like 1: ACE
RuvB-like 2: BDF
DNA methyltransferase 1-associated protein 1: G
Isoform 2 of E1A-binding protein p400: H
Actin-like protein 6A: IJ
Actin, cytoplasmic 1: K
Isoform 2 of Enhancer of polycomb homolog 1: L
Vacuolar protein sorting-associated protein 72 homolog: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

I
I

J
J

K
K

L
M

M
N

RuvB-like 1

RuvB-like 2

DNA methyltransferase 1-associated protein 1

Isoform 2 of E1A-binding protein p400

Actin-like protein 6A

Actin, cytoplasmic 1

Isoform 2 of Enhancer of polycomb homolog 1

Vacuolar protein sorting-associated protein 72 homolog

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