SMTL ID : 8qkv.1

SWR1-nucleosome complex in configuration 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 17 residues within 4Å: Chain L: N.695, L.696, R.697, Y.699, Q.700, M.723, G.724, L.725, G.726, K.727, T.728, I.729, N.1329, R.1357, I.1358 Ligands: BEF.2, MG.3 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:N.695, L:Q.700, L:G.724, L:L.725, L:G.726, L:K.727, L:T.728, L:T.728, L:T.728, L:N.1329 Salt bridges: L:K.727, L:R.1357, L:R.1357 ADP.4: 16 residues within 4Å: Chain M: G.11, S.12, Y.13, E.14, S.193, G.194, F.195, G.220, K.249, E.250, G.358, N.359, N.361, L.362 Ligands: BEF.5, MG.6 6 PLIP interactions: 6 interactions with chain M Hydrogen bonds: M:S.12, M:Y.13, M:F.195, M:K.249, M:G.358, M:N.361 ADP.9: 21 residues within 4Å: Chain O: A.26, H.29, G.47, V.49, G.80, P.81, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, E.379, I.383, R.387, R.413 Chain P: R.311, E.314, R.350 Ligands: MG.10 20 PLIP interactions: 17 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:A.26, O:H.29, O:V.49, O:S.82, 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:E.379, O:R.387, P:R.311, P:R.311, P:R.350 Salt bridges: O:K.85, O:R.413, O:R.413 ADP.11: 20 residues within 4Å: Chain P: 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, R.397 Chain Q: E.329, R.366 Ligands: MG.12 18 PLIP interactions: 16 interactions with chain P, 2 interactions with chain Q Hydrogen bonds: P:A.22, P:V.45, P:P.76, P:S.78, P:T.79, P:G.80, P:K.81, P:T.82, P:T.82, P:T.82, P:A.83, P:Y.359, Q:E.329 Salt bridges: P:H.23, P:K.81, P:R.397, P:R.397, Q:R.366 ADP.13: 19 residues within 4Å: Chain Q: A.26, H.27, 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 R: E.314 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain Q Hydrogen bonds: Q:A.26, Q:V.49, Q:G.80, Q:S.82, Q:T.83, Q:G.84, Q:K.85, Q:T.86, Q:A.87, Q:Y.375 Salt bridges: Q:H.27, Q:K.85, Q:R.413, Q:R.413 ADP.15: 19 residues within 4Å: 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, R.371, R.397 Chain S: R.366 Ligands: MG.16 18 PLIP interactions: 16 interactions with chain R, 2 interactions with chain S Hydrogen bonds: R:A.22, R:V.45, R:S.78, R:T.79, R:T.79, R:G.80, R:K.81, R:T.82, R:A.83, R:Y.359, R:R.371, R:R.397 Salt bridges: R:H.23, R:K.81, R:R.397, R:R.397, S:R.366, S:R.366 ADP.17: 19 residues within 4Å: Chain S: A.26, H.27, 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 T: E.314 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain S Hydrogen bonds: S:V.49, S:V.49, S:S.82, S:T.83, S:T.83, S:G.84, S:K.85, S:T.86, S:T.86, S:A.87, S:R.413 Salt bridges: S:K.85, S:R.413, S:R.413 pi-Stacking: S:Y.375 ADP.19: 18 residues within 4Å: Chain T: H.23, H.25, M.44, V.45, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, I.370, L.396, R.397 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain T Hydrogen bonds: T:V.45, T:S.78, T:T.79, T:G.80, T:K.81, T:T.82, T:T.82, T:A.83, T:E.297, T:Y.359, T:Y.359 Salt bridges: T:H.23, T:K.81, T:R.397 pi-Stacking: T:Y.359

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

BEF.2: 7 residues within 4Å: Chain L: M.723, K.727, G.1327, R.1354, R.1357 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 9 residues within 4Å: Chain M: G.11, S.12, Y.13, G.194, F.195, N.196, C.197 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain L: T.728 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain M: N.10, G.11, S.12 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain O: R.413 Chain P: R.311, R.350 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain P: T.82, N.326, R.397 Chain Q: R.366 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain Q: K.85, T.86 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.86 MG.16: 3 residues within 4Å: Chain R: K.81, T.82 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.82 MG.18: 3 residues within 4Å: Chain S: K.85, T.86 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.86 MG.20: 4 residues within 4Å: Chain T: T.82, D.296, E.297 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.82

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain N: C.244, C.247, C.264, S.265, C.268 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.244, N:C.247, N:C.264, N:C.268 ZN.8: 4 residues within 4Å: Chain N: C.256, C.259, H.272, C.277 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.256, N:C.259, N:H.272, N:C.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girvan, P. et al., Nucleosome flipping drives kinetic proofreading and processivity by SWR1. Nature (2024)

Release Date

2024-10-02

Peptides

Histone H3: AK
Histone H4: BC
Histone H2A.2: DJ
Histone H2B.1: EF
Vacuolar protein sorting-associated protein 72: I
Helicase SWR1: L
Actin-like protein ARP6: M
Vacuolar protein sorting-associated protein 71: N
RuvB-like protein 1: OQS
RuvB-like protein 2: PRT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
A

B
C

C
D

D
F

J
E

E
G

F
H

I
Z

L
M

M
R

N
S

O
T

Q
V

S
X

P
U

R
W

T
Y

Histone H3

Histone H4

Histone H2A.2

Histone H2B.1

Vacuolar protein sorting-associated protein 72

Helicase SWR1

Actin-like protein ARP6

Vacuolar protein sorting-associated protein 71

RuvB-like protein 1

RuvB-like protein 2

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