SMTL ID : 5ogw.1

Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

homo-pentamer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: G.16, S.17, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.17, A:N.19, A:Q.140, A:D.160, A:D.160, A:K.216, A:G.305, A:T.306, A:K.339 Salt bridges: A:K.21 ADP.4: 16 residues within 4Å: Chain B: G.16, S.17, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.17, B:N.19, B:Q.140, B:D.160, B:D.160, B:K.216, B:G.305, B:T.306, B:K.339 Salt bridges: B:K.21 ADP.6: 16 residues within 4Å: Chain C: G.16, S.17, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.17, C:N.19, C:Q.140, C:D.160, C:D.160, C:K.216, C:G.305, C:T.306, C:K.339 Salt bridges: C:K.21 ADP.9: 16 residues within 4Å: Chain D: G.16, S.17, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.17, D:N.19, D:Q.140, D:D.160, D:D.160, D:K.216, D:G.305, D:T.306, D:K.339 Salt bridges: D:K.21 ADP.11: 16 residues within 4Å: Chain E: G.16, S.17, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.17, E:N.19, E:Q.140, E:D.160, E:D.160, E:K.216, E:G.305, E:T.306, E:K.339 Salt bridges: E:K.21

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.140 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: Q.140 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: Q.140 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain D: Q.140 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain E: Q.140 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

3 x 9UE: Jasplakinolide(Non-covalent)

9UE.3: 17 residues within 4Å: Chain A: H.197, G.200, Y.201, G.202, F.203, E.208, L.245, N.249, I.251 Chain B: V.290 Chain D: H.76, I.78, L.113, P.115, G.117, R.180, D.182 10 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: D:I.78, D:I.78, D:P.115, B:V.290, A:F.203, A:L.245, A:N.249, A:I.251 Hydrogen bonds: D:D.182, A:G.200 9UE.8: 18 residues within 4Å: Chain A: V.290 Chain C: H.197, R.199, G.200, Y.201, G.202, F.203, E.208, L.245, N.249, I.251 Chain E: H.76, I.78, L.113, P.115, G.117, R.180, D.182 11 PLIP interactions: 6 interactions with chain C, 4 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: C:F.203, C:L.245, C:N.249, C:I.251, E:I.78, E:I.78, E:P.115, A:V.290 Hydrogen bonds: C:G.200, C:G.202, E:D.182 9UE.13: 17 residues within 4Å: Chain A: H.76, I.78, L.113, P.115, G.117, R.180, D.182 Chain D: V.290 Chain E: H.197, G.200, Y.201, G.202, F.203, E.208, L.245, N.249, I.251 10 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: E:F.203, E:L.245, E:N.249, E:I.251, D:V.290, A:I.78, A:I.78, A:P.115 Hydrogen bonds: E:G.200, A:D.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pospich, S. et al., Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-09-27

Peptides

Actin-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Actin-1

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