SMTL ID : 8qz0.1

SWR1-hexasome-dimer complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 20 residues within 4Å: Chain L: N.10, G.11, S.12, S.104, V.133, S.193, G.194, F.195, N.196, G.219, G.220, L.223, K.249, E.250, G.357, G.358, N.359, L.362 Ligands: BEF.2, MG.3 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:N.10, L:S.12, L:S.104, L:F.195, L:F.195, L:E.250, L:G.358, L:N.359 pi-Cation interactions: L:K.249 ADP.6: 20 residues within 4Å: Chain N: A.22, H.23, H.25, M.44, V.45, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, N.326, Y.359, I.367, L.396, R.397 Chain O: R.366 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:A.22, N:V.45, N:S.78, N:T.79, N:G.80, N:K.81, N:T.82, N:A.83, N:N.326, N:N.326, N:Y.359, O:R.366 Salt bridges: N:K.81, N:R.397, N:R.397 ADP.8: 19 residues within 4Å: Chain O: A.26, H.27, H.29, I.30, G.47, F.48, V.49, P.81, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, I.383, R.413 Chain P: E.314 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:H.27, O:V.49, O:S.82, O:T.83, O:G.84, O:K.85, O:T.86, O:T.86, O:A.87, O:Y.375 Salt bridges: O:K.85, O:K.85, O:R.413, O:R.413 ADP.10: 17 residues within 4Å: Chain P: A.22, H.23, H.25, M.44, V.45, G.46, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, R.397 Chain Q: E.329 Ligands: MG.11 14 PLIP interactions: 14 interactions with chain P Hydrogen bonds: P:A.22, P:V.45, P:G.46, P:S.78, P:T.79, P:G.80, P:K.81, P:T.82, P:T.82, P:A.83 Salt bridges: P:H.23, P:K.81, P:R.397, P:R.397 ADP.12: 20 residues within 4Å: Chain Q: A.26, H.27, H.29, I.30, G.47, F.48, V.49, G.80, P.81, S.82, T.83, G.84, K.85, T.86, A.87, N.341, Y.375, I.383, R.413 Ligands: MG.13 17 PLIP interactions: 17 interactions with chain Q Hydrogen bonds: Q:A.26, Q:H.27, Q:V.49, Q:S.82, Q:T.83, Q:T.83, Q:G.84, Q:K.85, Q:T.86, Q:A.87, Q:N.341, Q:Y.375, Q:Y.375 Salt bridges: Q:K.85, Q:K.85, Q:R.413, Q:R.413 ADP.14: 17 residues within 4Å: Chain R: A.22, H.23, H.25, G.43, M.44, V.45, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, R.397 14 PLIP interactions: 14 interactions with chain R Hydrogen bonds: R:A.22, R:V.45, R:P.76, R:S.78, R:T.79, R:G.80, R:K.81, R:T.82, R:T.82, R:A.83 Salt bridges: R:K.81, R:K.81, R:R.397, R:R.397 ADP.16: 19 residues within 4Å: Chain T: A.26, H.27, H.29, I.30, G.47, F.48, V.49, G.80, P.81, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, I.383, R.413 Ligands: MG.17 15 PLIP interactions: 15 interactions with chain T Hydrogen bonds: T:A.26, T:V.49, T:S.82, T:T.83, T:G.84, T:K.85, T:T.86, T:A.87, T:Y.375, T:Y.375, T:R.387 Salt bridges: T:K.85, T:K.85, T:R.413, T:R.413 ADP.18: 17 residues within 4Å: Chain U: R.697, Q.700, D.721, E.722, M.723, G.724, L.725, G.726, K.727, I.729, D.824, E.825, N.1329, R.1357, I.1358 Ligands: BEF.19, MG.20 16 PLIP interactions: 16 interactions with chain U Hydrogen bonds: U:R.697, U:Q.700, U:D.721, U:D.721, U:G.724, U:L.725, U:G.726, U:K.727, U:T.728, U:N.1329, U:N.1329, U:R.1357, U:R.1357, U:R.1357 Salt bridges: U:K.727, U:K.727

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 4 residues within 4Å: Chain L: S.12, Y.13, F.195 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) BEF.19: 8 residues within 4Å: Chain U: D.721, E.722, M.723, K.727, T.852, G.853 Ligands: ADP.18, MG.20 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain L: D.9 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain N: T.82 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain O: T.86, R.413 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.86 MG.11: 2 residues within 4Å: Chain P: T.82 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.82 MG.13: 2 residues within 4Å: Chain Q: T.86 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain R: T.325, N.326, R.327 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:T.325, R:R.327 MG.17: 2 residues within 4Å: Chain T: T.86 Ligands: ADP.16 No protein-ligand interaction detected (PLIP) MG.20: 6 residues within 4Å: Chain U: K.727, E.825, T.852, G.853 Ligands: ADP.18, BEF.19 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.852

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain M: C.244, S.245, I.246, C.247, G.248, C.268 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.244, M:C.247, M:C.268 ZN.5: 5 residues within 4Å: Chain M: C.256, N.258, C.259, G.260, R.276 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:C.256, M:C.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jalal, A.S.B. et al., Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex. Mol.Cell (2024)

Release Date

2024-10-02

Peptides

Histone H3: AB
Histone H4: CD
Histone H2A.1: E
Histone H2B.1: F
Histone H2B.1: G
Histone H2A.Z: J
SWR1-complex protein 5: K
Actin-like protein ARP6: L
Vacuolar protein sorting-associated protein 71: M
RuvB-like protein 2: NPR
RuvB-like protein 1: OQT
Vacuolar protein sorting-associated protein 72: S
Helicase SWR1: U
Histone H2A.Z-specific chaperone CHZ1: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

G
H

J
L

K
P

L
R

M
S

N
U

P
W

R
Y

O
V

Q
X

T
T

S
Z

U
M

V
K

Histone H3

Histone H4

Histone H2A.1

Histone H2B.1

Histone H2B.1

Histone H2A.Z

SWR1-complex protein 5

Actin-like protein ARP6

Vacuolar protein sorting-associated protein 71

RuvB-like protein 2

RuvB-like protein 1

Vacuolar protein sorting-associated protein 72

Helicase SWR1

Histone H2A.Z-specific chaperone CHZ1

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