SMTL ID : 7ahq.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: PO4.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.159, A:D.159, A:D.159, A:R.212, A:K.215, A:E.216, A:G.304, A:T.305, A:K.338, A:K.338 Salt bridges: A:K.20, A:K.20 ADP.5: 15 residues within 4Å: Chain B: S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: PO4.6, MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.159, B:D.159, B:D.159, B:R.212, B:K.215, B:E.216, B:G.304, B:T.305, B:K.338, B:K.338 Salt bridges: B:K.20, B:K.20 ADP.9: 15 residues within 4Å: Chain C: S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: PO4.10, MG.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.159, C:D.159, C:D.159, C:R.212, C:K.215, C:E.216, C:G.304, C:T.305, C:K.338, C:K.338 Salt bridges: C:K.20, C:K.20 ADP.13: 15 residues within 4Å: Chain D: S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: PO4.14, MG.15 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.159, D:D.159, D:D.159, D:R.212, D:K.215, D:E.216, D:G.304, D:T.305, D:K.338, D:K.338 Salt bridges: D:K.20, D:K.20 ADP.18: 15 residues within 4Å: Chain E: S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: PO4.19, MG.20 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.159, E:D.159, E:D.159, E:R.212, E:K.215, E:E.216, E:G.304, E:T.305, E:K.338, E:K.338 Salt bridges: E:K.20, E:K.20

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

PO4.2: 8 residues within 4Å: Chain A: G.15, S.16, Q.139, G.158, G.160, V.161 Ligands: ADP.1, MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.16, A:Q.139, A:G.160, A:V.161 PO4.6: 8 residues within 4Å: Chain B: G.15, S.16, Q.139, G.158, G.160, V.161 Ligands: ADP.5, MG.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.16, B:Q.139, B:G.160, B:V.161 PO4.10: 8 residues within 4Å: Chain C: G.15, S.16, Q.139, G.158, G.160, V.161 Ligands: ADP.9, MG.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.16, C:Q.139, C:G.160, C:V.161 PO4.14: 8 residues within 4Å: Chain D: G.15, S.16, Q.139, G.158, G.160, V.161 Ligands: ADP.13, MG.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.16, D:Q.139, D:G.160, D:V.161 PO4.19: 8 residues within 4Å: Chain E: G.15, S.16, Q.139, G.158, G.160, V.161 Ligands: ADP.18, MG.20 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.16, E:Q.139, E:G.160, E:V.161

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: Q.139 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.139 Ligands: ADP.5, PO4.6 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: Q.139 Ligands: ADP.9, PO4.10 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: Q.139 Ligands: ADP.13, PO4.14 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain E: Q.139 Ligands: ADP.18, PO4.19 No protein-ligand interaction detected (PLIP)

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(Non-covalent)(Covalent)

RLZ.4: 13 residues within 4Å: Chain A: E.74, H.75, I.77, T.79, L.112, P.114, A.116, R.179, D.181, M.271 Chain B: M.285, K.286, C.287 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.77, A:P.114, A:D.181 RLZ.8: 19 residues within 4Å: Chain A: G.199, Y.200, S.201, F.202, L.244, Q.248 Chain B: E.74, H.75, I.77, T.79, L.112, P.114, A.116, R.179, D.181, M.271 Chain C: M.285, K.286, C.287 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.200, A:F.202, B:I.77, B:P.114, B:D.181 Hydrogen bonds: A:G.199, A:S.201 RLZ.12: 20 residues within 4Å: Chain B: R.198, G.199, Y.200, S.201, F.202, L.244, Q.248 Chain C: E.74, H.75, I.77, T.79, L.112, P.114, A.116, R.179, D.181, M.271 Chain D: M.285, K.286, C.287 9 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:I.77, C:P.114, C:D.181, B:Y.200, B:F.202, B:L.244, D:K.286 Hydrogen bonds: B:G.199, B:S.201 RLZ.16: 18 residues within 4Å: Chain D: R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain E: E.74, H.75, I.77, T.79, L.112, P.114, A.116, R.179, D.181, M.271 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.202, E:I.77, E:P.114, E:D.181 Hydrogen bonds: D:G.199, D:S.201, D:S.201 RLZ.17: 21 residues within 4Å: Chain C: R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain D: E.74, H.75, I.77, T.79, L.112, P.114, A.116, R.179, D.181, M.271 Chain E: M.285, K.286, C.287 10 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:I.77, D:P.114, D:D.181, C:Y.200, C:F.202, E:M.285, E:K.286 Hydrogen bonds: C:G.199, C:S.201, C:S.201

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
A

B
B

C
C

D
D

E
E

Actin, alpha skeletal muscle

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