SMTL ID : 9b1d.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 12 residues within 4Å: Chain A: N.695, L.696, R.697, Q.700, M.723, G.724, G.726, K.727, T.728, I.729, F.767 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.695, A:R.697, A:G.724, A:G.726, A:K.727, A:K.727 Salt bridges: A:K.727 pi-Stacking: A:F.767 AGS.3: 16 residues within 4Å: Chain C: G.11, S.12, Y.13, E.14, K.16, G.194, F.195, N.196, N.246, K.249, E.250, G.357, G.358, N.359, N.361 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.12, C:Y.13, C:E.14, C:F.195, C:N.246, C:K.249, C:E.250, C:G.358, C:N.361 Salt bridges: C:K.16, C:K.16 AGS.7: 21 residues within 4Å: Chain E: A.26, H.27, H.29, G.47, F.48, V.49, S.82, T.83, G.84, K.85, T.86, A.87, E.312, N.341, Y.375, I.383, R.413, L.416 Chain F: D.346, R.350 Ligands: MG.8 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:H.27, E:V.49, E:S.82, E:T.83, E:G.84, E:K.85, E:K.85, E:T.86, E:T.86, E:A.87, E:E.312, E:E.312, E:N.341, E:Y.375, E:Y.375, F:R.350 Salt bridges: E:H.27, E:K.85 AGS.12: 20 residues within 4Å: Chain G: 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, N.341, Y.375, I.383, R.413, L.416 Chain H: R.350 Ligands: MG.11 21 PLIP interactions: 20 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:A.26, G:V.49, G:S.82, G:T.83, G:T.83, G:T.83, G:G.84, G:K.85, G:K.85, G:T.86, G:A.87, G:N.341, G:Y.375, G:Y.375, G:R.413, G:R.413, H:R.350 Salt bridges: G:H.27, G:K.85, G:R.413, G:R.413

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

MG.2: 2 residues within 4Å: Chain A: E.825 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.825 MG.4: 1 residues within 4Å: Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain E: T.86, D.311 Ligands: AGS.7 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.86, E:D.311, E:D.311 MG.9: 3 residues within 4Å: Chain F: T.82 Chain G: R.366 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.82 MG.11: 3 residues within 4Å: Chain G: T.86, D.311 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.86 MG.13: 4 residues within 4Å: Chain H: T.82, E.297 Chain I: R.366 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.82 MG.16: 4 residues within 4Å: Chain I: T.86, D.311 Chain J: E.314 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.86 MG.18: 4 residues within 4Å: Chain E: R.366 Chain J: T.82, D.296 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.82

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 5 residues within 4Å: Chain D: C.256, N.258, C.259, H.272, C.277 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.256, D:C.259, D:H.272

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

ADP.10: 20 residues within 4Å: Chain F: A.22, H.23, H.25, G.43, M.44, V.45, Q.47, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, I.367, L.396, R.397 Chain G: E.329 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:H.23, F:V.45, F:S.78, F:T.79, F:T.79, F:T.79, F:G.80, F:K.81, F:T.82, F:A.83, F:Y.359, F:Y.359 Salt bridges: F:H.23, F:K.81, F:R.397, F:R.397 ADP.14: 19 residues within 4Å: Chain H: A.22, H.23, H.25, G.43, M.44, V.45, Q.47, P.77, S.78, T.79, G.80, K.81, T.82, A.83, Y.359, L.396, R.397 Chain I: R.366 Ligands: MG.13 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:A.22, H:V.45, H:S.78, H:T.79, H:G.80, H:K.81, H:T.82, H:A.83, H:Y.359, H:Y.359, I:R.366 Salt bridges: H:H.23, H:K.81, H:R.397, H:R.397 ADP.15: 19 residues within 4Å: Chain I: A.26, H.27, H.29, G.47, F.48, V.49, Q.51, P.81, S.82, T.83, G.84, K.85, T.86, A.87, Y.375, I.383, R.413 Chain J: E.314 Ligands: MG.16 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:A.26, I:V.49, I:G.80, 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 Salt bridges: I:H.27, I:K.85, I:R.413, I:R.413 ADP.17: 18 residues within 4Å: Chain J: 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, I.367, R.397 Ligands: MG.18 16 PLIP interactions: 14 interactions with chain J, 2 interactions with chain E Hydrogen bonds: J:A.22, J:V.45, J:S.78, J:T.79, J:G.80, J:K.81, J:T.82, J:A.83, J:Y.359, J:Y.359, E:E.329, E:E.329 Salt bridges: J:H.23, J:K.81, J:R.397, J:R.397

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

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

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

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