SMTL ID : 8qyv.1

SWR1-hexasome complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 17 residues within 4Å: Chain I: N.695, R.697, Q.700, G.724, L.725, G.726, K.727, T.728, I.729, N.759, R.766, F.767, N.1329, R.1357, I.1358 Ligands: BEF.2, MG.3 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:N.695, I:R.697, I:Q.700, I:G.724, I:G.724, I:G.726, I:K.727, I:T.728, I:T.728, I:T.728, I:N.759, I:N.1329, I:N.1329 Salt bridges: I:K.727, I:R.1357 pi-Stacking: I:F.767 pi-Cation interactions: I:R.697 ADP.4: 15 residues within 4Å: Chain K: G.11, S.12, Y.13, E.14, G.194, F.195, N.196, K.249, E.250, G.358, N.359, N.361, L.362 Ligands: BEF.5, MG.6 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:G.11, K:S.12, K:S.12, K:Y.13, K:E.14, K:F.195, K:N.196, K:K.249, K:E.250, K:E.250, K:G.358, K:N.361 ADP.9: 19 residues within 4Å: Chain M: A.26, H.27, H.29, G.47, F.48, V.49, Q.51, G.80, P.81, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, I.383, R.413 Ligands: MG.10 14 PLIP interactions: 1 interactions with chain N, 13 interactions with chain M Hydrogen bonds: N:E.314, M:A.26, M:V.49, M:V.49, M:S.82, M:T.83, M:G.84, M:K.85, M:T.86, M:A.87, M:Y.375 Salt bridges: M:K.85, M:R.413, M:R.413 ADP.11: 18 residues within 4Å: Chain N: A.22, H.23, H.25, G.43, M.44, V.45, P.77, S.78, T.79, G.80, K.81, T.82, A.83, N.326, Y.359, I.367, R.397 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain N Hydrogen bonds: N:A.22, N:V.45, N:S.78, N:T.79, N:G.80, N:K.81, N:T.82, N:T.82, N:A.83, N:N.326, N:N.326, N:Y.359, N:Y.359 Salt bridges: N:K.81, N:R.397, N:R.397 ADP.13: 18 residues within 4Å: Chain O: A.26, H.27, H.29, 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.14 17 PLIP interactions: 17 interactions with chain O Hydrogen bonds: O:A.26, O:H.27, O:V.49, O:S.82, O:T.83, O:T.83, O:G.84, O:K.85, O:T.86, O:T.86, O:T.86, O:A.87, O:Y.375, O:Y.375 Salt bridges: O:K.85, O:R.413, O:R.413 ADP.15: 17 residues within 4Å: Chain P: A.22, H.23, H.25, G.43, M.44, V.45, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, R.397 Chain Q: R.366 Ligands: MG.16 15 PLIP interactions: 14 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:A.22, P:V.45, P:S.78, P:T.79, P:G.80, P:K.81, P:T.82, P:T.82, P:A.83, P:Y.359, P:Y.359 Salt bridges: P:K.81, P:R.397, P:R.397, Q:R.366 ADP.17: 18 residues within 4Å: Chain Q: A.26, H.27, H.29, I.30, G.47, F.48, V.49, G.80, S.82, T.83, G.84, K.85, T.86, Y.375, I.383, R.413 Chain R: R.350 Ligands: MG.18 16 PLIP interactions: 15 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:A.26, Q:V.49, Q:S.82, Q:T.83, Q:G.84, Q:K.85, Q:T.86, Q:T.86, Q:A.87, Q:Y.375, Q:Y.375 Salt bridges: Q:K.85, Q:K.85, Q:R.413, Q:R.413, R:R.350 ADP.19: 19 residues within 4Å: Chain M: R.366 Chain R: A.22, H.23, H.25, I.26, G.43, M.44, V.45, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, R.397 Ligands: MG.20 14 PLIP interactions: 13 interactions with chain R, 1 interactions with chain M Hydrogen bonds: R:V.45, R:S.78, R:T.79, R:G.80, R:K.81, R:T.82, R:T.82, R:A.83, R:Y.359, R:Y.359 Salt bridges: R:K.81, R:R.397, R:R.397, M:R.366

2 x BEF: BERYLLIUM TRIFLUORIDE ION

BEF.2: 9 residues within 4Å: Chain I: E.722, M.723, G.724, L.725, K.727, R.1354, R.1357 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 4 residues within 4Å: Chain K: N.10, N.196 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION

MG.3: 5 residues within 4Å: Chain I: K.727, D.824, E.825 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.825 MG.6: 4 residues within 4Å: Chain K: N.10, G.11 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain M: T.86 Chain N: R.350 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.86 MG.12: 3 residues within 4Å: Chain N: T.82, D.296 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.82 MG.14: 4 residues within 4Å: Chain O: K.85, T.86, R.413 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain P: T.82, D.296 Chain Q: R.366 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.82 MG.18: 2 residues within 4Å: Chain Q: T.86 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.86 MG.20: 4 residues within 4Å: Chain M: R.366 Chain R: T.82, D.296 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.82

2 x ZN: ZINC ION

ZN.7: 4 residues within 4Å: Chain L: C.244, I.246, C.247, C.268 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.244, L:C.247, L:C.268 ZN.8: 4 residues within 4Å: Chain L: C.256, C.259, H.272, C.277 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.256, L:C.259, L:H.272, L:C.277

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
Helicase SWR1: I
SWR1-complex protein 5: J
Actin-like protein ARP6: K
Vacuolar protein sorting-associated protein 71: L
RuvB-like protein 1: MOQ
RuvB-like protein 2: NPR
Vacuolar protein sorting-associated protein 72: S

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

I
M

J
P

K
R

L
S

M
T

O
V

Q
X

N
U

P
W

R
Y

S
Z

Histone H3

Histone H4

Histone H2A.1

Histone H2B.1

Helicase SWR1

SWR1-complex protein 5

Actin-like protein ARP6

Vacuolar protein sorting-associated protein 71

RuvB-like protein 1

RuvB-like protein 2

Vacuolar protein sorting-associated protein 72

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