SMTL ID : 9b1e.1

Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: N.695, R.697, 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.700, A:Q.700, A:G.724, A:L.725, A:G.726, A:K.727, A:T.728, A:T.728, A:T.728, A:R.766, A:R.766, A:N.1329 Salt bridges: A:R.1357 pi-Cation interactions: A:R.697 ADP.4: 15 residues within 4Å: Chain C: G.11, S.12, Y.13, E.14, K.16, G.194, F.195, N.196, K.249, E.250, G.358, N.361, A.393 Ligands: BEF.5, MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.12, C:Y.13, C:E.14, C:E.14, C:F.195, C:N.196, C:K.249, C:E.250, C:N.361 Salt bridges: C:K.16, C:K.16 ADP.9: 17 residues within 4Å: Chain E: A.26, H.27, H.29, G.47, F.48, V.49, G.80, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, I.383, L.416 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:A.26, E:V.49, E:S.82, E:T.83, E:G.84, E:K.85, E:T.86, E:T.86, E:A.87, E:Y.375 Salt bridges: E:K.85 ADP.11: 19 residues within 4Å: Chain F: 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, Y.359, L.396, R.397 Chain G: R.366 Ligands: MG.12 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:H.23, F:V.45, F:S.78, F:T.79, F:G.80, F:K.81, F:T.82, F:T.82, F:A.83, F:Y.359, F:Y.359, G:R.366 Salt bridges: F:H.23, F:K.81, F:R.397, F:R.397 ADP.13: 19 residues within 4Å: Chain G: 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, R.387, R.413 Chain H: R.350 Ligands: MG.14 17 PLIP interactions: 16 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:A.26, G:H.27, G:V.49, G:S.82, G:T.83, G:G.84, G:K.85, G:T.86, G:T.86, G:A.87, G:Y.375, G:Y.375, G:R.387, H:R.350 Salt bridges: G:K.85, G:R.413, G:R.413 ADP.15: 20 residues within 4Å: Chain H: H.23, H.25, G.43, M.44, V.45, Q.47, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, R.371, L.396, R.397 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:H.25, H:V.45, H:S.78, H:T.79, H:G.80, H:K.81, H:T.82, H:T.82, H:A.83, H:Y.359, H:Y.359 Salt bridges: H:H.23, H:K.81, H:R.397, H:R.397 ADP.17: 20 residues within 4Å: Chain I: 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, L.416 Chain J: E.314 Ligands: MG.18 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:A.26, I:V.49, I:S.82, I:T.83, I:G.84, I:K.85, I:T.86, I:T.86, I:A.87, I:Y.375, I:Y.375, J:E.314 Salt bridges: I:H.27, I:K.85, I:R.413, I:R.413 ADP.19: 21 residues within 4Å: Chain E: E.329 Chain J: A.22, H.23, H.25, G.43, M.44, V.45, Q.47, P.76, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, L.396, R.397 Ligands: MG.20 15 PLIP interactions: 14 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:H.23, J:V.45, J:V.45, J:S.78, J:T.79, J:G.80, J:K.81, J:T.82, J:A.83, J:Y.359, E:E.329 Salt bridges: J:H.23, J:K.81, J:R.397, J:R.397

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

BEF.2: 5 residues within 4Å: Chain A: M.723, G.724, R.1357 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 6 residues within 4Å: Chain C: N.10, G.11, S.12, N.196 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 2 residues within 4Å: 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: 2 residues within 4Å: Chain E: T.86 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: T.82 Chain G: E.329, R.366 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.82 MG.14: 3 residues within 4Å: Chain G: T.86, D.311 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.86 MG.16: 3 residues within 4Å: Chain H: T.82, R.397 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.82 MG.18: 4 residues within 4Å: Chain I: R.413 Chain J: E.314, R.350 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: K.81, T.82 Ligands: ADP.19 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Louder, R.K. et al., Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler. Cell(Cambridge,Mass.) (2024)

Release Date

2024-10-09

Peptides

Helicase SWR1: A
Vacuolar protein sorting-associated protein 72: B
Actin-like protein ARP6: C
Vacuolar protein sorting-associated protein 71: D
RuvB-like protein 1: EGI
RuvB-like protein 2: FHJ
SWR1-complex protein 3: K
Histone H2A: LN
Histone H2B: MO
Histone H3: PR
Histone H4: QS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

G
G

I
I

F
F

H
H

J
J

K
K

L
Q

N
S

M
R

O
T

P
U

R
W

Q
V

S
X

Helicase SWR1

Vacuolar protein sorting-associated protein 72

Actin-like protein ARP6

Vacuolar protein sorting-associated protein 71

RuvB-like protein 1

RuvB-like protein 2

SWR1-complex protein 3

Histone H2A

Histone H2B

Histone H3

Histone H4

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