SMTL ID : 9fbw.1

SWR1 lacking Swc5 subunit in complex with hexasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 18 residues within 4Å: Chain I: R.697, Q.700, M.723, G.724, L.725, G.726, K.727, T.728, I.729, N.759, E.763, L.1326, G.1327, I.1328, R.1354, R.1357 Ligands: BEF.2, MG.3 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:Q.700, I:G.724, I:E.763, I:E.763, I:I.1328, I:R.1357 Salt bridges: I:K.727, I:R.1354, I:R.1354 ADP.4: 15 residues within 4Å: Chain J: G.11, S.12, Y.13, E.14, G.194, F.195, N.196, C.197, G.358, N.359, N.361, L.362, D.391 Ligands: BEF.5, MG.6 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.12, J:S.12, J:E.14, J:E.14, J:F.195, J:N.196, J:C.197, J:N.361, J:N.361 Salt bridges: J:K.16 ADP.9: 21 residues within 4Å: Chain L: A.26, H.27, H.29, I.30, G.47, F.48, V.49, Q.51, G.80, P.81, S.82, T.83, G.84, K.85, T.86, Y.375, E.379, I.383, R.413 Chain M: E.314, R.350 17 PLIP interactions: 15 interactions with chain L, 2 interactions with chain M Hydrogen bonds: L:A.26, L:H.27, L:V.49, L:V.49, L:Q.51, L:G.80, L:G.80, L:S.82, L:T.83, L:T.83, L:G.84, L:K.85, L:T.86, L:R.413, M:E.314, M:R.350 Salt bridges: L:K.85 ADP.11: 18 residues within 4Å: Chain M: 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 17 PLIP interactions: 1 interactions with chain N, 16 interactions with chain M Salt bridges: N:K.326, M:R.397, M:R.397 Hydrogen bonds: M:A.22, M:H.23, M:V.45, M:S.78, M:T.79, M:G.80, M:K.81, M:T.82, M:A.83, M:N.326, M:N.326, M:Y.359, M:Y.359 pi-Stacking: M:H.23 ADP.13: 15 residues within 4Å: Chain N: 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 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:H.27, N:V.49, N:S.82, N:T.83, N:T.83, N:T.83, N:G.84, N:K.85, N:T.86, N:A.87, N:Y.375 Salt bridges: N:K.85 ADP.15: 18 residues within 4Å: Chain O: A.22, H.23, H.25, I.26, M.44, V.45, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, L.396 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:H.23, O:V.45, O:V.45, O:P.76, O:S.78, O:T.79, O:K.81, O:T.82, O:A.83 Salt bridges: O:K.81, O:K.81 ADP.17: 15 residues within 4Å: Chain P: A.26, H.27, H.29, I.30, F.48, G.80, P.81, S.82, T.83, G.84, K.85, T.86, Y.375, R.386, R.413 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:A.26, P:H.27, P:S.82, P:T.83, P:T.83, P:G.84, P:K.85, P:T.86, P:R.386 Salt bridges: P:R.413, P:R.413 ADP.19: 22 residues within 4Å: Chain L: E.329, R.366 Chain Q: 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, D.296, Y.359, I.367, R.371, R.397 Ligands: MG.20 17 PLIP interactions: 14 interactions with chain Q, 3 interactions with chain L Hydrogen bonds: Q:A.22, Q:H.23, Q:V.45, Q:V.45, Q:S.78, Q:G.80, Q:K.81, Q:T.82, Q:T.82, Q:T.82, Q:A.83, L:E.329, L:E.329 Salt bridges: Q:H.23, Q:R.397, Q:R.397, L:R.366

2 x BEF: BERYLLIUM TRIFLUORIDE ION

BEF.2: 9 residues within 4Å: Chain I: M.723, K.727, D.824, E.825, G.853, L.1326, R.1354 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 8 residues within 4Å: Chain J: S.12, D.192, G.194, F.195, N.196, C.197, T.198 Ligands: ADP.4 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION

MG.3: 4 residues within 4Å: Chain I: K.727, T.728 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain J: D.192, S.193, G.357, G.358, A.393 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.193 MG.10: 3 residues within 4Å: Chain M: N.310, E.314, R.350 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain M: T.82, R.397 Chain N: E.329 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain N: G.84, K.85, T.86 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain O: T.82, A.83 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.82 MG.18: 4 residues within 4Å: Chain P: K.85, T.86, D.311 Chain Q: R.311 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:T.86, P:D.311 MG.20: 4 residues within 4Å: Chain L: R.366 Chain Q: T.82, D.296 Ligands: ADP.19 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:T.82, Q:D.296

2 x ZN: ZINC ION

ZN.7: 6 residues within 4Å: Chain K: C.244, I.246, C.247, I.263, S.265, C.268 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.244, K:C.247, K:C.268 ZN.8: 4 residues within 4Å: Chain K: C.256, C.259, H.272, C.277 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.256, K:C.259, K:H.272, K: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
Actin-like protein ARP6: J
Vacuolar protein sorting-associated protein 71: K
RuvB-like protein 1: LNP
RuvB-like protein 2: MOQ
Vacuolar protein sorting-associated protein 72: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

I
M

J
R

K
S

L
T

N
V

P
X

M
U

O
W

Q
Y

R
Z

Histone H3

Histone H4

Histone H2A.1

Histone H2B.1

Helicase SWR1

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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