SMTL ID : 8qku.1

SWR1-nucleosome complex in configuration 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 16 residues within 4Å: Chain K: N.695, L.696, Q.700, M.723, G.724, L.725, G.726, K.727, T.728, I.729, R.766, N.1329, R.1357, I.1358 Ligands: BEF.2, MG.3 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:Q.700, K:Q.700, K:G.724, K:L.725, K:G.726, K:K.727, K:T.728, K:T.728, K:I.729, K:R.766, K:R.766, K:N.1329 Salt bridges: K:K.727, K:R.1357, K:R.1357 ADP.4: 16 residues within 4Å: Chain L: G.11, S.12, Y.13, E.14, K.16, G.194, F.195, G.220, N.246, K.249, E.250, G.358, N.359, L.362 Ligands: BEF.5, MG.6 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.11, L:S.12, L:Y.13, L:E.14, L:F.195, L:N.246, L:K.249, L:E.250, L:G.358 Salt bridges: L:K.16, L:K.16 ADP.9: 19 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, I.383, R.413 Chain O: E.314, R.350 Ligands: MG.10 18 PLIP interactions: 16 interactions with chain N, 2 interactions with chain O Hydrogen bonds: N:A.26, N:V.49, N:S.82, N:T.83, N:T.83, N:G.84, N:K.85, N:T.86, N:T.86, N:T.86, N:A.87, N:Y.375, N:Y.375 Salt bridges: N:K.85, N:R.413, N:R.413, O:R.350, O:R.350 ADP.11: 20 residues within 4Å: Chain O: 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, N.326, Y.359, I.367, R.397 Chain P: R.366 Ligands: MG.12 16 PLIP interactions: 15 interactions with chain O, 1 interactions with chain P Hydrogen bonds: O:A.22, O:V.45, O:S.78, O:T.79, O:G.80, O:K.81, O:T.82, O:T.82, O:A.83, O:N.326, O:N.326, O:Y.359, P:R.366 Salt bridges: O:K.81, O:R.397, O:R.397 ADP.13: 18 residues within 4Å: Chain P: 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 Q: E.314 Ligands: MG.14 16 PLIP interactions: 16 interactions with chain P Hydrogen bonds: P:A.26, P:V.49, P:S.82, P:T.83, P:T.83, P:T.83, P:G.84, P:K.85, P:T.86, P:T.86, P:A.87, P:Y.375, P:Y.375, P:R.413 Salt bridges: P:R.413, P:R.413 ADP.15: 19 residues within 4Å: Chain Q: A.22, H.23, H.25, I.26, G.43, V.45, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, L.396, R.397 Chain R: R.366 Ligands: MG.16 15 PLIP interactions: 14 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:A.22, Q:V.45, Q:S.78, Q:T.79, Q:G.80, Q:T.82, Q:T.82, Q:A.83, Q:Y.359, Q:Y.359 Salt bridges: Q:H.23, Q:K.81, Q:K.81, Q:R.397, R:R.366 ADP.17: 18 residues within 4Å: Chain R: A.26, H.29, 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 Chain S: R.350 Ligands: MG.18 17 PLIP interactions: 16 interactions with chain R, 1 interactions with chain S Hydrogen bonds: R:A.26, R:V.49, R:S.82, R:T.83, R:T.83, R:G.84, R:K.85, R:T.86, R:T.86, R:A.87, R:Y.375, R:Y.375 Salt bridges: R:K.85, R:K.85, R:R.413, R:R.413, S:R.350 ADP.19: 22 residues within 4Å: Chain N: E.329, R.366 Chain S: 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, N.326, Y.359, I.367, L.396, R.397 Ligands: MG.20 17 PLIP interactions: 15 interactions with chain S, 2 interactions with chain N Hydrogen bonds: S:H.25, S:V.45, S:S.78, S:T.79, S:G.80, S:K.81, S:T.82, S:T.82, S:N.326, S:Y.359, S:Y.359, N:R.366 Salt bridges: S:K.81, S:R.397, S:R.397, N:R.366 pi-Stacking: S:Y.359

2 x BEF: BERYLLIUM TRIFLUORIDE ION

BEF.2: 7 residues within 4Å: Chain K: M.723, K.727, G.1327, R.1354, R.1357 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 6 residues within 4Å: Chain L: S.12, G.194, F.195, N.196 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION

MG.3: 4 residues within 4Å: Chain K: K.727, T.728 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.728 MG.6: 2 residues within 4Å: Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain N: R.413 Chain O: R.350 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain O: T.82, R.397 Chain P: E.329, R.366 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.82 MG.14: 2 residues within 4Å: Chain P: T.86 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.86 MG.16: 3 residues within 4Å: Chain Q: T.82 Chain R: R.366 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.82 MG.18: 2 residues within 4Å: Chain R: T.86 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.86 MG.20: 4 residues within 4Å: Chain N: R.366 Chain S: T.82, E.297 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.82

2 x ZN: ZINC ION

ZN.7: 4 residues within 4Å: Chain M: C.244, C.247, C.264, C.268 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.244, M:C.247, M:C.264, M:C.268 ZN.8: 4 residues within 4Å: Chain M: C.256, C.259, H.272, C.277 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.256, M:C.259, M:H.272, M:C.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girvan, P. et al., Nucleosome flipping drives kinetic proof reading and processivity of histone exchange by yeast SWR1 complex. To Be Published

Release Date

2024-10-02

Peptides

Histone H3: AB
Histone H4: CD
Histone H2A.2: EF
Histone H2B.1: GH
Helicase SWR1: K
Actin-like protein ARP6: L
Vacuolar protein sorting-associated protein 71: M
RuvB-like protein 1: NPR
RuvB-like protein 2: OQS
Vacuolar protein sorting-associated protein 72: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

K
M

L
R

M
S

N
T

P
V

R
X

O
U

Q
W

S
Y

T
Z

Histone H3

Histone H4

Histone H2A.2

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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