SMTL ID : 6uxw.1

SWI/SNF nucleosome complex with ADP-BeFx

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-1-1-4-1-1-5-1-mer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain K: H.15, D.190, A.224, Q.229, K.232 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:D.190, K:D.190, K:Q.229 Water bridges: K:R.16 Salt bridges: K:H.15, K:K.232 PO4.2: 4 residues within 4Å: Chain K: N.53, Y.89, T.93, Q.94 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:N.53, K:Y.89, K:Q.94 PO4.3: 9 residues within 4Å: Chain K: H.15, R.16, G.160, A.161, G.186, K.232, S.397, T.398 Ligands: PO4.1 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:S.397, K:S.397, K:S.397, K:T.398, K:T.398, K:T.398 Water bridges: K:A.161, K:A.161, K:K.232, K:K.232 Salt bridges: K:H.15, K:R.16, K:K.232 PO4.4: 4 residues within 4Å: Chain K: H.11, G.13, E.141 Ligands: PO4.5 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:E.141, K:E.141 Water bridges: K:S.14, K:R.16, K:A.161, K:A.161, K:G.436 Salt bridges: K:H.11 PO4.5: 9 residues within 4Å: Chain K: S.14, G.75, D.158, G.160, A.161, S.162, N.165, R.181 Ligands: PO4.4 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:S.14, K:S.14, K:D.158, K:A.161, K:S.162, K:S.162, K:N.165 Water bridges: K:H.15 Salt bridges: K:R.181 PO4.6: 8 residues within 4Å: Chain L: S.16, Q.17, N.70, G.71, G.165, T.166, H.167, H.168 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:S.16, L:Q.17, L:Q.17, L:T.166, L:T.166, L:H.167, L:H.168 Water bridges: L:S.16, L:S.16 Salt bridges: L:H.167, L:H.168 PO4.7: 5 residues within 4Å: Chain L: R.15, G.338, S.425, E.426 Ligands: PO4.9 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:G.338, L:S.425, L:E.426, L:E.426 Salt bridges: L:R.15 PO4.8: 3 residues within 4Å: Chain L: S.343, G.344, K.346 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:G.344 Water bridges: L:F.345, L:K.346 Salt bridges: L:K.346 PO4.9: 7 residues within 4Å: Chain L: Y.13, R.15, D.163, V.164, G.337, G.338 Ligands: PO4.7 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:Y.13, L:D.163, L:G.338 Salt bridges: L:R.15 PO4.10: 5 residues within 4Å: Chain L: D.206, D.208, Q.209, D.286, K.288 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.208 Salt bridges: L:K.288 PO4.11: 5 residues within 4Å: Chain K: K.293 Chain L: G.314, D.318, D.356, H.357 5 PLIP interactions: 1 interactions with chain K, 4 interactions with chain L Salt bridges: K:K.293, L:H.357 Hydrogen bonds: L:G.314 Water bridges: L:L.315, L:L.315 PO4.12: 2 residues within 4Å: Chain K: D.431 Chain N: R.619 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain N Hydrogen bonds: K:D.431, K:D.431 Salt bridges: N:R.619, N:K.623

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

ADP.13: 17 residues within 4Å: Chain N: T.766, K.768, Y.770, D.792, G.795, L.796, G.797, K.798, T.799, I.800, W.838, N.1171, Q.1173, R.1199, I.1200 Ligands: BEF.14, MG.15 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:T.766, N:Y.770, N:G.795, N:L.796, N:G.797, N:K.798, N:T.799, N:T.799, N:T.799, N:N.1171, N:N.1171, N:Q.1173, N:R.1199 Salt bridges: N:K.798, N:R.1199

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

BEF.14: 6 residues within 4Å: Chain N: L.1170, N.1171, R.1196, R.1199 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 4 residues within 4Å: Chain N: D.894, E.895 Ligands: ADP.13, BEF.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y. et al., Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature (2020)

Release Date

2020-03-18

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Actin-related protein 7: K
Actin-like protein ARP9: L
Regulator of Ty1 transposition protein 102: M
Transcription regulatory protein SNF2: N
SWI/SNF chromatin-remodeling complex subunit SWI1: O
SWI/SNF chromatin-remodeling complex subunit SNF5: P
SWI/SNF complex subunit SWI3: QRST
Transcription regulatory protein SNF12: U
Transcription regulatory protein SNF6: V
Unknown protein: WXY01
SWI/SNF global transcription activator complex subunit SWP82: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

E
V

B
S

F
W

C
T

G
X

D
U

H
Y

K
P

L
Q

M
Z

N
A

O
B

P
C

Q
D

R
E

S
F

T
G

U
H

V
I

W
J

X
K

Y
L

0
N

1
O

Z
M

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Actin-related protein 7

Actin-like protein ARP9

Regulator of Ty1 transposition protein 102

Transcription regulatory protein SNF2

SWI/SNF chromatin-remodeling complex subunit SWI1

SWI/SNF chromatin-remodeling complex subunit SNF5

SWI/SNF complex subunit SWI3

Transcription regulatory protein SNF12

Transcription regulatory protein SNF6

Unknown protein

SWI/SNF global transcription activator complex subunit SWP82

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