SMTL ID : 9g9t.1

Cryo-EM structure of the Toxoplasma gondii respiratory chain complex III inhibited by ELQ-300

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

16 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 36 residues within 4Å: Chain A: N.19, S.20, S.21, F.24, L.27, F.80, L.83, C.84, L.86, I.87, T.90, R.91, Y.94, N.95, P.196, K.217, C.218, Y.221, L.222, L.225, W.259, V.321, Y.322, M.324, I.325, I.328 Chain G: R.116 Chain H: K.86, Y.90, W.94, V.95, G.98, L.99, F.102 Ligands: CDL.14, CDL.15 Ligand excluded by PLIP CDL.9: 49 residues within 4Å: Chain C: F.325, F.328, M.329, S.332, F.335, I.336, T.337, S.339, M.340, M.341, R.342, S.343, F.344 Chain I: F.64, M.86, G.90, L.93, V.94, S.95, S.96, W.97, W.99, S.100 Chain M: V.33, L.34, I.37, I.223, F.227 Chain N: Y.359, K.362, C.363, A.366, I.367, I.369, L.373 Chain V: V.36, I.40, M.43, W.44, F.47, P.48, L.58, T.59, F.60, I.62, W.63 Ligands: PC1.8, CDL.16, CDL.27 Ligand excluded by PLIP CDL.10: 46 residues within 4Å: Chain C: E.226, G.227, W.228, F.229, K.230, R.231, R.233 Chain M: V.312, V.313, S.314, W.316, I.319, Y.322, S.323, F.326, L.345, A.346, I.348, L.349 Chain S: K.34, R.38, L.41, S.42, L.45, W.49, F.53, R.54, L.57 Chain T: W.96, P.97, I.100, T.101, L.104 Chain W: A.125, V.126, V.128, T.129, L.130, P.132, L.133, M.135, F.136, A.139, F.140, F.141 Chain X: V.83 Ligand excluded by PLIP CDL.11: 23 residues within 4Å: Chain A: M.2, F.5, R.6, V.10, V.33, I.37, Y.208, L.212 Chain D: R.502, A.503, F.505, W.506, L.507, R.508 Chain O: F.334, M.341, F.344, L.345 Chain S: W.160, Y.161 Ligands: CDL.26, CDL.29, PC1.32 Ligand excluded by PLIP CDL.13: 40 residues within 4Å: Chain A: L.4, T.103, M.106, S.107, L.109, V.110, L.113, L.114, A.117, L.142, I.176, I.179, I.180, V.182, L.183, Y.187, F.281, M.282, L.285, I.286, G.289 Chain G: T.166, H.176, F.177, L.178, L.181 Chain L: G.57, T.58, V.59, L.60, M.61, V.64, V.67, F.68, A.71 Chain M: F.1 Chain S: L.181, L.184 Ligands: CDL.17, CDL.30 Ligand excluded by PLIP CDL.14: 32 residues within 4Å: Chain A: K.217, Y.221, G.224, L.225, L.228 Chain B: V.364, A.368, T.371, V.372, T.375, L.376, W.378, R.379 Chain F: F.10 Chain H: I.72, Y.73, F.75, W.76, H.77, F.79, F.80, R.82, C.83, K.86, C.87, Y.90, A.91, V.95 Chain U: I.33, F.35 Ligands: CDL.1, CDL.15 Ligand excluded by PLIP CDL.15: 27 residues within 4Å: Chain B: S.365, A.368, I.369, V.372, L.373, L.376 Chain H: L.69, K.70, F.71, I.72, Y.73, P.74, W.76 Chain O: R.322, F.325 Chain U: R.55, K.58, D.59, M.60, F.61, F.64, F.65, W.99, W.102 Ligands: CDL.1, CDL.14, CDL.26 Ligand excluded by PLIP CDL.16: 25 residues within 4Å: Chain C: R.322, F.325 Chain I: R.55, K.58, D.59, M.60, F.61, F.64, F.65, W.99, W.102 Chain N: S.365, A.368, I.369, V.372, L.376 Chain T: K.70, F.71, I.72, Y.73, P.74, W.76 Ligands: CDL.9, CDL.18, CDL.31 Ligand excluded by PLIP CDL.17: 33 residues within 4Å: Chain G: H.154, M.155, W.156, E.157, W.160, Y.161, F.168, L.178 Chain I: N.81, C.85 Chain L: T.58, V.59, L.60, P.62, I.63, V.64, R.66, V.67 Chain M: M.2 Chain P: L.507, R.508, Y.509 Chain V: R.20, W.24, I.27, W.28, R.30, V.31, W.34, W.38 Ligands: PC1.8, CDL.13, CDL.27 Ligand excluded by PLIP CDL.18: 36 residues within 4Å: Chain M: N.19, S.20, S.21, F.24, L.27, F.80, L.83, C.84, L.86, I.87, T.90, R.91, Y.94, N.95, P.196, K.217, C.218, Y.221, L.222, L.225, W.259, V.321, Y.322, M.324, I.325, I.328 Chain S: R.116 Chain T: K.86, Y.90, W.94, V.95, G.98, L.99, F.102 Ligands: CDL.16, CDL.31 Ligand excluded by PLIP CDL.25: 46 residues within 4Å: Chain A: V.312, V.313, S.314, W.316, I.319, Y.322, S.323, F.326, L.345, A.346, I.348, L.349 Chain G: K.34, R.38, L.41, S.42, L.45, W.49, F.53, R.54, L.57 Chain H: W.96, P.97, I.100, T.101, L.104 Chain K: A.125, V.126, V.128, T.129, L.130, P.132, L.133, M.135, F.136, A.139, F.140, F.141 Chain L: V.83 Chain O: E.226, G.227, W.228, F.229, K.230, R.231, R.233 Ligand excluded by PLIP CDL.26: 49 residues within 4Å: Chain A: V.33, L.34, I.37, I.223, F.227 Chain B: Y.359, K.362, C.363, A.366, I.367, I.369, L.373 Chain J: V.36, I.40, M.43, W.44, F.47, P.48, L.58, T.59, F.60, I.62, W.63 Chain O: F.325, F.328, M.329, S.332, F.335, I.336, T.337, S.339, M.340, M.341, R.342, S.343, F.344 Chain U: F.64, M.86, G.90, L.93, V.94, S.95, S.96, W.97, W.99, S.100 Ligands: CDL.11, CDL.15, PC1.32 Ligand excluded by PLIP CDL.27: 23 residues within 4Å: Chain C: F.334, M.341, F.344, L.345 Chain G: W.160, Y.161 Chain M: M.2, F.5, R.6, V.10, V.33, I.37, Y.208, L.212 Chain P: R.502, A.503, F.505, W.506, L.507, R.508 Ligands: PC1.8, CDL.9, CDL.17 Ligand excluded by PLIP CDL.29: 33 residues within 4Å: Chain A: M.2 Chain D: L.507, R.508, Y.509 Chain J: R.20, W.24, I.27, W.28, R.30, V.31, W.34, W.38 Chain S: H.154, M.155, W.156, E.157, W.160, Y.161, F.168, L.178 Chain U: N.81, C.85 Chain X: T.58, V.59, L.60, P.62, I.63, V.64, R.66, V.67 Ligands: CDL.11, CDL.30, PC1.32 Ligand excluded by PLIP CDL.30: 40 residues within 4Å: Chain A: F.1 Chain G: L.181, L.184 Chain M: L.4, T.103, M.106, S.107, L.109, V.110, L.113, L.114, A.117, L.142, I.176, I.179, I.180, V.182, L.183, Y.187, F.281, M.282, L.285, I.286, G.289 Chain S: T.166, H.176, F.177, L.178, L.181 Chain X: G.57, T.58, V.59, L.60, M.61, V.64, V.67, F.68, A.71 Ligands: CDL.13, CDL.29 Ligand excluded by PLIP CDL.31: 33 residues within 4Å: Chain I: I.33, F.35 Chain M: K.217, Y.221, G.224, L.225, L.228 Chain N: V.364, I.367, A.368, T.371, V.372, T.375, L.376, W.378, R.379 Chain R: F.10 Chain T: I.72, Y.73, F.75, W.76, H.77, F.79, F.80, R.82, C.83, K.86, C.87, Y.90, A.91, V.95 Ligands: CDL.16, CDL.18 Ligand excluded by PLIP

4 x 01: 6-chloranyl-7-methoxy-2-methyl-3-[4-[4-(trifluoromethyloxy)phenoxy]phenyl]-1~{H}-quinolin-4-one

01.2: 21 residues within 4Å: Chain A: H.8, L.9, Y.12, C.14, L.18, N.19, Y.22, N.23, F.26, C.178, I.181, V.182, I.185, L.188, H.189, S.193, F.207, M.211, T.214, D.215 Ligands: HEM.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.9, A:F.26, A:F.207 Hydrogen bonds: A:H.189, A:D.215 pi-Stacking: A:F.207 01.3: 20 residues within 4Å: Chain A: L.86, M.89, T.90, L.93, Y.112, L.113, I.116, I.138, F.261, Y.264, Y.265, L.268, F.281, S.284, L.285, L.288, V.317, W.320, Y.350, L.357 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.116, A:Y.264, A:Y.264, A:F.281, A:L.285 Hydrogen bonds: A:Y.112 pi-Stacking: A:Y.112, A:W.320 Halogen bonds: A:T.90, A:F.261 01.19: 20 residues within 4Å: Chain M: H.8, L.9, Y.12, L.18, N.19, Y.22, N.23, F.26, C.178, I.181, V.182, I.185, L.188, H.189, S.193, F.207, M.211, T.214, D.215 Ligands: HEM.22 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:L.9, M:F.26, M:F.207 Hydrogen bonds: M:H.189, M:D.215 pi-Stacking: M:F.207 01.20: 20 residues within 4Å: Chain M: L.86, M.89, T.90, L.93, Y.112, L.113, I.116, I.138, F.261, Y.264, Y.265, L.268, F.281, S.284, L.285, L.288, V.317, W.320, Y.350, L.357 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:I.116, M:Y.264, M:Y.264, M:F.281, M:L.285 Hydrogen bonds: M:Y.112 pi-Stacking: M:Y.112, M:W.320 Halogen bonds: M:T.90, M:F.261

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.4: 28 residues within 4Å: Chain A: F.32, Q.35, I.36, G.39, I.40, L.42, A.43, Y.46, V.57, R.71, H.74, A.75, A.78, V.81, F.82, T.115, T.118, A.119, G.122, Y.123, L.125, P.126, F.167, H.170, F.171, P.174, F.175, Y.260 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Q.35, A:I.40, A:T.118, A:L.125, A:F.171, A:P.174 Water bridges: A:R.71, A:R.71, A:R.71 Salt bridges: A:R.71, A:R.71 Metal complexes: A:H.74, A:H.170 HEM.5: 28 residues within 4Å: Chain A: Y.22, F.24, G.25, F.26, V.28, A.29, F.32, I.85, H.88, M.89, R.91, G.92, S.97, L.101, A.104, W.105, G.108, L.109, L.111, Y.112, T.115, I.181, H.184, I.185, L.188, S.193, S.194 Ligands: 01.2 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:V.28, A:F.32, A:L.101, A:W.105, A:L.109, A:I.181, A:L.188, A:L.188 Hydrogen bonds: A:Y.22, A:F.24, A:G.25, A:S.97, A:S.193, A:S.194, A:S.194 Water bridges: A:F.26, A:H.88, A:S.193 Salt bridges: A:H.88, A:R.91, A:R.91 Metal complexes: A:H.88, A:H.184 HEM.21: 28 residues within 4Å: Chain M: F.32, Q.35, I.36, G.39, I.40, L.42, A.43, Y.46, V.57, R.71, H.74, A.75, A.78, V.81, F.82, T.115, T.118, A.119, G.122, Y.123, L.125, P.126, F.167, H.170, F.171, P.174, F.175, Y.260 13 PLIP interactions: 13 interactions with chain M, Hydrophobic interactions: M:Q.35, M:I.40, M:T.118, M:L.125, M:F.171, M:P.174 Water bridges: M:R.71, M:R.71, M:R.71 Salt bridges: M:R.71, M:R.71 Metal complexes: M:H.74, M:H.170 HEM.22: 28 residues within 4Å: Chain M: Y.22, F.24, G.25, F.26, V.28, A.29, F.32, I.85, H.88, M.89, R.91, G.92, S.97, L.101, A.104, W.105, G.108, L.109, L.111, Y.112, T.115, I.181, H.184, I.185, L.188, S.193, S.194 Ligands: 01.19 22 PLIP interactions: 22 interactions with chain M, Hydrophobic interactions: M:V.28, M:F.32, M:L.101, M:W.105, M:L.109, M:I.181, M:L.188, M:L.188 Hydrogen bonds: M:F.24, M:G.25, M:S.97, M:S.193, M:S.194, M:S.194 Water bridges: M:F.26, M:H.88, M:S.193 Salt bridges: M:H.88, M:R.91, M:R.91 Metal complexes: M:H.88, M:H.184

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 6 residues within 4Å: Chain A: R.295, N.298, T.299, R.300, M.301, Y.360 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.295, A:N.298, A:R.300, A:Y.360, H2O.18 MG.23: 6 residues within 4Å: Chain M: R.295, N.298, T.299, R.300, M.301, Y.360 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:R.295, M:N.298, M:R.300, M:Y.360, H2O.4

2 x HEC: HEME C(Covalent)

HEC.7: 27 residues within 4Å: Chain B: V.187, V.191, C.192, T.194, C.195, H.196, N.260, A.263, Y.264, P.265, P.266, L.268, I.271, R.275, Y.281, L.282, L.285, L.286, F.308, I.313, A.314, M.315, P.316, P.318, L.319, V.341, L.345 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:P.265, B:I.313, B:M.315, B:P.318 Hydrogen bonds: B:Y.281, B:Y.281, B:A.314 Salt bridges: B:R.275 pi-Stacking: B:H.196 Metal complexes: B:H.196 HEC.24: 27 residues within 4Å: Chain N: V.187, V.191, C.192, T.194, C.195, H.196, N.260, A.263, Y.264, P.265, P.266, L.268, I.271, R.275, Y.281, L.282, L.285, L.286, F.308, I.313, A.314, M.315, P.316, P.318, L.319, V.341, L.345 10 PLIP interactions: 10 interactions with chain N, Hydrophobic interactions: N:P.265, N:I.313, N:M.315, N:P.318 Hydrogen bonds: N:Y.281, N:Y.281, N:A.314 Salt bridges: N:R.275 pi-Stacking: N:H.196 Metal complexes: N:H.196

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.8: 36 residues within 4Å: Chain C: Y.327, S.330, Y.333, F.334, T.337, A.338, M.341 Chain I: Y.74, L.78, K.79, D.80, N.81, Y.84, C.85, V.88, M.89 Chain M: F.26, M.30, V.33, Y.208, L.212, M.213, A.216, L.219 Chain N: M.374, W.377 Chain P: H.479, D.480, R.502, F.505, L.507 Chain V: W.38, F.41 Ligands: CDL.9, CDL.17, CDL.27 14 PLIP interactions: 5 interactions with chain C, 3 interactions with chain P, 3 interactions with chain M, 3 interactions with chain I Hydrophobic interactions: C:F.334, C:A.338, C:M.341, M:F.26, M:Y.208, M:L.219, I:Y.84 Hydrogen bonds: C:S.330, I:N.81, I:Y.84 pi-Cation interactions: C:Y.327, P:F.505 Salt bridges: P:R.502, P:R.502 PC1.32: 36 residues within 4Å: Chain A: F.26, M.30, V.33, Y.208, L.212, M.213, A.216, L.219 Chain B: M.374, W.377 Chain D: H.479, D.480, R.502, F.505, L.507 Chain J: W.38, F.41 Chain O: Y.327, S.330, Y.333, F.334, T.337, A.338, M.341 Chain U: Y.74, L.78, K.79, D.80, N.81, Y.84, C.85, V.88, M.89 Ligands: CDL.11, CDL.26, CDL.29 16 PLIP interactions: 3 interactions with chain U, 3 interactions with chain A, 3 interactions with chain D, 5 interactions with chain O, 2 interactions with chain J Hydrophobic interactions: U:Y.84, A:F.26, A:Y.208, A:L.219, O:F.334, O:A.338, O:M.341, J:W.38, J:F.41 Hydrogen bonds: U:N.81, U:Y.84, O:S.330 Salt bridges: D:R.502, D:R.502 pi-Cation interactions: D:F.505, O:Y.327

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain D: H.113, E.116, H.117, E.193 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.113, D:H.117, H2O.6 ZN.28: 4 residues within 4Å: Chain P: H.113, E.116, H.117, E.193 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.113, P:H.117, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

MacLean, A.E. et al., Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-06-18

Peptides

Cytochrome b: AM
Cytochrome c1, heme protein: BN
Putative ubiquinol cytochrome c oxidoreductase: CO
Putative peptidase M16 family protein: DP
Alpha-MPP: EQ
Putative ubiquinol-cytochrome c reductase hinge protein: FR
Ubiquinol-cytochrome c reductase: GS
QCR8/TGGT1_227910: HT
Ubiquinol-cytochrome C family reductase UQCRX/QCR9-like protein: IU
Transmembrane protein: JV
Transmembrane protein: KW
Transmembrane protein: LX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M
a

B
B

N
b

C
C

O
c

D
D

P
d

E
E

Q
e

F
F

R
f

G
G

S
g

H
H

T
h

I
I

U
i

J
J

V
j

K
K

W
k

L
L

X
l

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b

Cytochrome c1, heme protein

Putative ubiquinol cytochrome c oxidoreductase

Putative peptidase M16 family protein

Alpha-MPP

Putative ubiquinol-cytochrome c reductase hinge protein

Ubiquinol-cytochrome c reductase

QCR8/TGGT1_227910

Ubiquinol-cytochrome C family reductase UQCRX/QCR9-like protein

Transmembrane protein

Transmembrane protein

Transmembrane protein

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