SMTL ID : 6gej.1

Chromatin remodeller-nucleosome complex at 3.6 A resolution.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 17 residues within 4Å: Chain L: N.695, L.696, R.697, Q.700, M.723, G.724, L.725, G.726, K.727, T.728, I.729, N.1329, R.1354, R.1357, I.1358 Ligands: BEF.2, MG.3 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:R.697, L:Q.700, L:Q.700, L:G.724, L:G.726, L:K.727, L:T.728, L:T.728, L:T.728, L:R.1354, L:R.1357 Salt bridges: L:K.727, L:R.1357, L:R.1357 pi-Cation interactions: L:R.697 ADP.4: 16 residues within 4Å: Chain M: G.11, S.12, Y.13, E.14, K.16, F.195, N.196, N.246, K.249, E.250, G.358, N.361, L.362, A.393 Ligands: BEF.5, MG.6 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:S.12, M:Y.13, M:E.14, M:F.195, M:N.196, M:N.246, M:K.249, M:E.250, M:G.358, M:N.361 Salt bridges: M:K.16, M:K.16 ADP.9: 17 residues within 4Å: Chain O: 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, R.413 Chain P: E.314 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:A.26, 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, O:Y.375 Salt bridges: O:K.85, O:R.413, O:R.413 ADP.11: 19 residues within 4Å: Chain P: A.22, 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 Q: E.329 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:A.22, P:V.45, P:V.45, 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:N.326 Salt bridges: P:K.81, P:R.397, P:R.397 ADP.13: 17 residues within 4Å: Chain Q: 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, 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:S.82, 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:R.413, Q:R.413 ADP.15: 17 residues within 4Å: Chain R: A.22, H.25, G.43, M.44, V.45, P.77, S.78, T.79, G.80, K.81, T.82, Y.359, I.367, R.397 Chain S: E.329, R.366 Ligands: MG.16 16 PLIP interactions: 14 interactions with chain R, 2 interactions with chain S Hydrogen bonds: R:A.22, R:V.45, R:S.78, R:T.79, R:G.80, R:T.82, R:T.82, R:T.82, R:A.83, R:Y.359, R:Y.359, S:R.366 Salt bridges: R:K.81, R:R.397, R:R.397, S:R.366 ADP.17: 18 residues within 4Å: Chain S: A.26, H.29, G.47, F.48, V.49, G.80, P.81, S.82, T.83, G.84, K.85, T.86, Y.375, I.383, R.413, L.416 Chain T: E.314 Ligands: MG.18 14 PLIP interactions: 14 interactions with chain S Hydrogen bonds: S:H.29, S:V.49, S:G.80, S:S.82, S:T.83, S:G.84, S:K.85, S:T.86, S:T.86, S:Y.375, S:Y.375 Salt bridges: S:K.85, S:R.413, S:R.413 ADP.19: 18 residues within 4Å: Chain O: E.329, R.366 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, R.397 Ligands: MG.20 14 PLIP interactions: 13 interactions with chain T, 1 interactions with chain O Hydrogen bonds: T:H.25, T:V.45, T:V.45, T:S.78, T:T.79, T:G.80, T:T.82, T:T.82, T:A.83, O:R.366 Salt bridges: T:K.81, T:R.397, T:R.397 pi-Stacking: T:Y.359

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

BEF.2: 8 residues within 4Å: Chain L: M.723, G.724, K.727, Q.1350, R.1354, R.1357 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 7 residues within 4Å: Chain M: S.12, 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)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain L: D.824 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain O: T.86 Chain P: E.314, R.350 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain P: T.82, D.296 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.82 MG.14: 4 residues within 4Å: Chain Q: K.85, T.86, D.311 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.86 MG.16: 4 residues within 4Å: Chain R: T.82, E.297 Chain S: R.366 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.297 MG.18: 3 residues within 4Å: Chain S: T.86, D.311 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 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:T.82, T:D.296, T:D.296, T:E.297

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain N: C.244, I.246, C.247, C.264, 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

Willhoft, O. et al., Structure and dynamics of the yeast SWR1-nucleosome complex. Science (2018)

Release Date

2018-10-17

Peptides

Vacuolar protein sorting-associated protein 72: A
Histone H3: BC
Histone H4: DE
Histone H2A.1: FG
Histone H2B.1: HI
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
Z

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

L
M

M
R

N
S

O
T

Q
V

S
X

P
U

R
W

T
Y

Vacuolar protein sorting-associated protein 72

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

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