SMTL ID : 7ahn.1

Cryo-EM structure of F-actin stabilized by cis-optoJASP-8

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2, PO4.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:D.159, A:D.159, A:D.159, A:K.215, A:E.216, A:G.304, A:T.305 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.5: 19 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6, PO4.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:E.216, B:G.304, B:T.305 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.10: 19 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.11, PO4.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:D.159, C:D.159, C:D.159, C:K.215, C:E.216, C:G.304, C:T.305 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.14: 19 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.15, PO4.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:L.18, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:G.304, D:T.305 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.18: 19 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.19, PO4.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.16, E:G.17, E:L.18, E:L.18, E:D.159, E:D.159, E:D.159, E:K.215, E:E.216, E:G.304, E:T.305 Salt bridges: E:K.20, E:K.20 pi-Stacking: E:Y.308

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.13, Q.139 Ligands: ADP.1, PO4.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: D.13, Q.139 Ligands: ADP.5, PO4.7 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.13, Q.139 Ligands: ADP.10, PO4.12 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: D.13, Q.139 Ligands: ADP.14, PO4.16 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain E: D.13, Q.139 Ligands: ADP.18, PO4.20 No protein-ligand interaction detected (PLIP)

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

PO4.3: 9 residues within 4Å: Chain A: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.1, MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.16, A:Q.139, A:G.158, A:D.159, A:G.160, A:V.161 PO4.7: 9 residues within 4Å: Chain B: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.5, MG.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.16, B:Q.139, B:G.158, B:D.159, B:G.160, B:V.161 PO4.12: 9 residues within 4Å: Chain C: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.10, MG.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.16, C:Q.139, C:G.158, C:D.159, C:G.160, C:V.161 PO4.16: 9 residues within 4Å: Chain D: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.14, MG.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.16, D:Q.139, D:G.158, D:D.159, D:G.160, D:V.161 PO4.20: 9 residues within 4Å: Chain E: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.18, MG.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.16, E:Q.139, E:G.158, E:D.159, E:G.160, E:V.161

5 x RLZ: ~{N}-[4-[(4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-2,6,9,12-tetrakis(oxidanylidene)-1-oxa-5,8,11-triazacyclononadec-15-en-10-yl]butyl]-~{N}'-[5-methoxy-2-[(~{Z})-(3,4,5-trimethoxyphenyl)diazenyl]phenyl]butanediamide(Covalent)(Non-covalent)

RLZ.4: 21 residues within 4Å: Chain A: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 Chain C: I.289, R.292 Chain D: E.74, H.75, I.77, L.112, P.114, A.116, N.117, R.179, D.181 11 PLIP interactions: 3 interactions with chain D, 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:I.77, D:I.77, D:P.114, A:T.196, A:Y.200, A:F.202, A:L.244, C:I.289 Hydrogen bonds: A:G.199, A:S.201, A:S.201 RLZ.8: 12 residues within 4Å: Chain B: E.74, H.75, I.77, L.112, P.114, A.116, N.117, R.179, D.181 Chain E: M.285, I.289, R.292 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:I.289, B:I.77, B:I.77, B:P.114 RLZ.9: 21 residues within 4Å: Chain A: I.289, R.292 Chain B: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 Chain E: E.74, H.75, I.77, L.112, P.114, A.116, N.117, R.179, D.181 11 PLIP interactions: 7 interactions with chain B, 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: B:T.196, B:Y.200, B:F.202, B:L.244, E:I.77, E:I.77, E:P.114, A:I.289 Hydrogen bonds: B:G.199, B:S.201, B:S.201 RLZ.13: 18 residues within 4Å: Chain C: E.74, H.75, I.77, L.112, P.114, A.116, R.179, D.181 Chain D: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.77, C:I.77, C:P.114, D:T.196, D:F.202, D:L.244 Hydrogen bonds: D:G.199, D:S.201 RLZ.17: 22 residues within 4Å: Chain A: E.74, H.75, I.77, L.112, P.114, A.116, N.117, R.179, D.181 Chain D: M.285, I.289, R.292 Chain E: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 10 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: E:T.196, E:F.202, E:L.244, D:I.289, A:I.77, A:I.77, A:P.114 Hydrogen bonds: E:G.199, E:S.201, D:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pospich, S. et al., Cryo-EM Resolves Molecular Recognition Of An Optojasp Photoswitch Bound To Actin Filaments In Both Switch States. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-01-27

Peptides

Actin, alpha skeletal muscle: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
E

D
D

E
B

Actin, alpha skeletal muscle

Related Entries With Identical Sequence