SMTL ID : 6bnq.1

CryoEM structure of Myosin VI-Actin complex in the ADP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain G: Q.139, D.156 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.156 MG.3: 3 residues within 4Å: Chain H: Q.139, D.156 Ligands: ADP.4 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.156, H:D.156 MG.5: 3 residues within 4Å: Chain I: Q.139, D.156 Ligands: ADP.6 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.156, I:D.156 MG.7: 3 residues within 4Å: Chain J: Q.139, D.156 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.156, J:D.156 MG.9: 4 residues within 4Å: Chain K: S.16, Q.139, D.156 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.156, K:D.156 MG.11: 4 residues within 4Å: Chain L: S.16, Q.139, D.156 Ligands: ADP.12 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.156, L:D.156 MG.13: 3 residues within 4Å: Chain M: Q.139, D.156 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.156 MG.15: 3 residues within 4Å: Chain N: Q.139, D.156 Ligands: ADP.16 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.156, N:D.156

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

ADP.2: 20 residues within 4Å: Chain G: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:D.13, G:S.16, G:G.17, G:L.18, G:D.159, G:R.185, G:R.212, G:K.215, G:G.304, G:T.305, G:M.307 Salt bridges: G:K.20, G:K.20 pi-Stacking: G:Y.308 ADP.4: 19 residues within 4Å: Chain H: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:D.13, H:S.16, H:G.17, H:L.18, H:Q.139, H:R.212, H:K.215, H:G.304, H:T.305, H:M.307 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308 ADP.6: 19 residues within 4Å: Chain I: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:S.16, I:G.17, I:L.18, I:Q.139, I:Q.139, I:R.212, I:K.215, I:G.304, I:T.305, I:M.307 Salt bridges: I:K.20, I:K.20 pi-Stacking: I:Y.308 ADP.8: 18 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:D.13, J:S.16, J:G.17, J:L.18, J:Q.139, J:K.215, J:G.304, J:T.305, J:M.307, J:K.338 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308 ADP.10: 19 residues within 4Å: Chain K: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:D.13, K:S.16, K:G.17, K:L.18, K:Q.139, K:K.215, K:G.304, K:T.305 Salt bridges: K:K.20, K:K.20 pi-Stacking: K:Y.308 ADP.12: 19 residues within 4Å: Chain L: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:D.13, L:S.16, L:G.17, L:L.18, L:Q.139, L:R.212, L:K.215, L:G.304, L:T.305, L:M.307 Salt bridges: L:K.20, L:K.20 pi-Stacking: L:Y.308 ADP.14: 18 residues within 4Å: Chain M: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:D.13, M:S.16, M:G.17, M:K.215, M:G.304, M:T.305, M:M.307 Salt bridges: M:K.20, M:K.20 pi-Stacking: M:Y.308 ADP.16: 20 residues within 4Å: Chain N: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:D.13, N:S.16, N:G.17, N:L.18, N:Q.139, N:K.215, N:G.304, N:T.305, N:M.307 Salt bridges: N:K.20, N:K.20 pi-Stacking: N:Y.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gurel, P.S. et al., Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity. Elife (2017)

Release Date

2018-01-10

Peptides

Unconventional myosin-VI: ABCDEF
Actin, alpha skeletal muscle: GHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

Unconventional myosin-VI

Actin, alpha skeletal muscle

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