SMTL ID : 9h8t.1

Cryo-EM structure of the atovaquone-inhibited Complex III from the Chlorocebus sabaeus respirasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-2-2-2-2-2-2-2-2-mer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: V.116, V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, I.211, L.214, L.215, F.237, I.242, A.243, M.244, P.247, I.248, V.270, L.274 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:N.189, A:P.194, A:P.195, A:I.200, A:L.214, A:I.242, A:M.244, A:I.248 Hydrogen bonds: A:Y.210, A:A.243 Salt bridges: A:R.204 Metal complexes: A:H.125 HEC.14: 26 residues within 4Å: Chain L: V.116, V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, I.211, L.214, L.215, F.237, I.242, A.243, M.244, P.247, I.248, V.270, L.274 12 PLIP interactions: 12 interactions with chain L, Hydrophobic interactions: L:N.189, L:P.194, L:P.195, L:I.200, L:L.214, L:I.242, L:M.244, L:I.248 Hydrogen bonds: L:Y.210, L:A.243 Salt bridges: L:R.204 Metal complexes: L:H.125

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.284, M.288 Chain H: H.75, W.77 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A Metal complexes: H:H.75, A:H.284 ZN.15: 3 residues within 4Å: Chain L: H.284, M.288 Chain S: H.75 2 PLIP interactions: 1 interactions with chain S, 1 interactions with chain L Metal complexes: S:H.75, L:H.284

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 11 residues within 4Å: Chain B: C.217, H.219, L.220, G.221, C.222, C.236, C.238, H.239, G.240, S.241, P.253 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.217, B:H.219, B:C.236, B:H.239 FES.16: 11 residues within 4Å: Chain M: C.217, H.219, L.220, G.221, C.222, C.236, C.238, H.239, G.240, S.241, P.253 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.217, M:H.219, M:C.236, M:H.239

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 28 residues within 4Å: Chain A: F.101, I.300, Y.304 Chain C: H.73 Chain D: M.38, R.41, V.42, S.45, F.46, V.49, V.50, V.54, Y.57, L.58 Chain H: S.28, M.29, W.30, Y.104, L.230, L.234, F.237, I.238, T.241, L.242, L.245, S.246, L.249 Ligands: PEE.7 9 PLIP interactions: 4 interactions with chain H, 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: H:F.237, H:L.245, D:V.50, A:Y.304 Hydrogen bonds: H:M.29, H:W.30 Salt bridges: D:R.41, D:R.41, C:H.73 CDL.12: 25 residues within 4Å: Chain H: R.5, L.18, I.19, S.35, L.36, A.38, F.39, I.42, F.220, H.221, T.225, D.228, I.229, L.232 Chain I: F.370, R.470, W.477, L.478, R.479 Chain J: W.24, G.28 Ligands: PC1.5, PEE.8, AFI.9, PEE.13 10 PLIP interactions: 3 interactions with chain I, 7 interactions with chain H Hydrogen bonds: I:L.478, I:R.479 Salt bridges: I:R.479, H:R.5, H:H.221 Hydrophobic interactions: H:F.39, H:I.42, H:T.225, H:D.228, H:I.229 CDL.17: 28 residues within 4Å: Chain L: F.101, I.300, Y.304 Chain N: H.73 Chain O: M.38, R.41, V.42, S.45, F.46, V.49, V.50, V.54, Y.57, L.58 Chain S: S.28, M.29, W.30, Y.104, L.230, L.234, F.237, I.238, T.241, L.242, L.245, S.246, L.249 Ligands: PEE.20 8 PLIP interactions: 3 interactions with chain O, 4 interactions with chain S, 1 interactions with chain N Hydrophobic interactions: O:V.50, S:F.237, S:L.245 Salt bridges: O:R.41, O:R.41, N:H.73 Hydrogen bonds: S:M.29, S:W.30 CDL.25: 26 residues within 4Å: Chain S: R.5, L.18, I.19, S.35, L.36, A.38, F.39, I.42, F.220, H.221, T.225, D.228, I.229, L.232 Chain T: F.370, R.470, W.477, L.478, R.479 Chain U: W.24, G.28, L.32 Ligands: PC1.18, PEE.21, AFI.22, PEE.26 10 PLIP interactions: 7 interactions with chain S, 3 interactions with chain T Hydrophobic interactions: S:F.39, S:I.42, S:T.225, S:D.228, S:I.229 Salt bridges: S:R.5, S:H.221, T:R.479 Hydrogen bonds: T:L.478, T:R.479

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

PC1.5: 30 residues within 4Å: Chain A: M.306, K.310 Chain E: F.15, R.16, T.18, F.21, A.22, I.25, V.26 Chain I: D.451, F.476, L.478 Chain J: W.24, V.27, G.31, L.32, W.34, A.35 Chain M: Y.115, T.118, T.122, V.125, A.126, A.129, K.130, V.133, T.134, I.137 Ligands: CDL.12, PEE.13 11 PLIP interactions: 7 interactions with chain M, 1 interactions with chain I, 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: M:T.122, M:V.125, M:A.129, M:V.133, M:T.134, E:I.25 Hydrogen bonds: M:T.118 pi-Cation interactions: M:Y.115, I:F.476, E:F.21 Salt bridges: A:K.310 PC1.18: 31 residues within 4Å: Chain B: Y.115, T.118, T.122, V.125, A.126, A.129, K.130, V.133, T.134, I.137 Chain L: M.306, K.310 Chain P: F.15, R.16, T.18, F.21, A.22, I.25, V.26 Chain T: D.451, F.476, L.478 Chain U: W.24, V.27, G.28, G.31, L.32, W.34, A.35 Ligands: CDL.25, PEE.26 11 PLIP interactions: 8 interactions with chain B, 1 interactions with chain T, 2 interactions with chain P Hydrophobic interactions: B:T.122, B:V.125, B:A.129, B:V.133, B:T.134, B:I.137, P:V.26 Hydrogen bonds: B:T.118 pi-Cation interactions: B:Y.115, T:F.476, P:F.21

2 x AOQ: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione(Non-covalent)

AOQ.6: 21 residues within 4Å: Chain B: C.238, H.239 Chain H: F.121, M.124, F.128, Y.131, M.138, W.141, G.142, V.145, I.146, L.149, I.268, P.270, F.274, A.277, Y.278, L.281, L.294, F.295, I.298 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:F.128, H:I.268, H:F.274, H:A.277 Hydrogen bonds: B:H.239 AOQ.19: 21 residues within 4Å: Chain M: C.238, H.239 Chain S: F.121, M.124, F.128, Y.131, M.138, W.141, G.142, V.145, I.146, L.149, I.268, P.270, F.274, A.277, Y.278, L.281, L.294, F.295, I.298 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain M Hydrophobic interactions: S:F.128, S:I.268, S:F.274, S:A.277 Hydrogen bonds: M:H.239

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.7: 26 residues within 4Å: Chain C: N.70 Chain D: S.45, V.49, F.53 Chain H: W.30, I.92, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, L.250, W.272, L.301, M.316, F.325, W.326, I.329, L.332, L.333, Y.358 Ligands: CDL.4 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:L.96, H:V.98, H:W.272, H:L.301, H:W.326 Hydrogen bonds: H:Y.103 PEE.8: 12 residues within 4Å: Chain H: M.4 Chain I: F.370, G.374, W.477, R.479 Chain J: W.24, G.25, V.27, G.28, T.29, L.32 Ligands: CDL.12 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J, 1 interactions with chain H Hydrophobic interactions: I:R.479, J:W.24, J:L.32 Salt bridges: I:R.479 Hydrogen bonds: H:M.4 PEE.13: 20 residues within 4Å: Chain A: M.296, L.299 Chain H: H.221, T.225, I.229, L.232, V.233, L.236 Chain I: S.473, G.474, F.476, W.477, L.478 Chain M: V.125, A.128, A.129, V.132, V.133 Ligands: PC1.5, CDL.12 10 PLIP interactions: 4 interactions with chain I, 4 interactions with chain H, 1 interactions with chain M, 1 interactions with chain A Hydrophobic interactions: I:L.478, H:I.229, H:I.229, H:L.236, M:V.125, A:L.299 Hydrogen bonds: I:S.473, I:S.473, I:S.473 Salt bridges: H:H.221 PEE.20: 26 residues within 4Å: Chain N: N.70 Chain O: S.45, V.49, F.53 Chain S: W.30, I.92, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, L.250, W.272, L.301, M.316, F.325, W.326, I.329, L.332, L.333, Y.358 Ligands: CDL.17 6 PLIP interactions: 6 interactions with chain S Hydrophobic interactions: S:L.96, S:V.98, S:W.272, S:L.301, S:W.326 Hydrogen bonds: S:Y.103 PEE.21: 11 residues within 4Å: Chain S: M.4 Chain T: F.370, G.374, W.477, R.479 Chain U: W.24, G.25, G.28, T.29, L.32 Ligands: CDL.25 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain S Hydrophobic interactions: T:R.479 Salt bridges: T:R.479 Hydrogen bonds: S:M.4 PEE.26: 20 residues within 4Å: Chain B: V.125, A.128, A.129, V.132, V.133 Chain L: M.296, L.299 Chain S: H.221, T.225, I.229, L.232, V.233, L.236 Chain T: S.473, G.474, F.476, W.477, L.478 Ligands: PC1.18, CDL.25 10 PLIP interactions: 1 interactions with chain B, 4 interactions with chain S, 4 interactions with chain T, 1 interactions with chain L Hydrophobic interactions: B:V.125, S:I.229, S:I.229, S:L.236, T:L.478, L:L.299 Salt bridges: S:H.221 Hydrogen bonds: T:S.473, T:S.473, T:S.473

2 x AFI: 2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE(Non-covalent)

AFI.9: 16 residues within 4Å: Chain H: L.18, L.21, T.23, I.27, W.31, S.35, A.38, I.42, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEM.11, CDL.12 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:L.18, H:I.42, H:F.220, H:F.220 Hydrogen bonds: H:H.201, H:D.228 Water bridges: H:S.35 pi-Stacking: H:F.220 AFI.22: 16 residues within 4Å: Chain S: L.18, L.21, T.23, I.27, W.31, S.35, A.38, I.42, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEM.24, CDL.25 8 PLIP interactions: 8 interactions with chain S Hydrophobic interactions: S:L.18, S:I.42, S:F.220, S:F.220 Hydrogen bonds: S:H.201, S:D.228 Water bridges: S:S.35 pi-Stacking: S:F.220

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

HEM.10: 29 residues within 4Å: Chain H: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.84, A.87, F.90, F.91, T.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, Y.273 11 PLIP interactions: 11 interactions with chain H, Hydrophobic interactions: H:Q.44, H:I.45, H:A.52, H:F.90, H:T.126, H:L.133, H:F.183 Salt bridges: H:R.80, H:R.80 Metal complexes: H:H.83, H:H.182 HEM.11: 30 residues within 4Å: Chain H: W.31, G.34, S.35, L.37, A.38, L.41, F.90, L.94, H.97, V.98, R.100, G.101, S.106, L.109, T.112, W.113, G.116, I.117, L.119, L.120, T.123, I.189, T.193, H.196, L.197, L.200, S.205, N.206, L.301 Ligands: AFI.9 23 PLIP interactions: 23 interactions with chain H, Hydrophobic interactions: H:L.37, H:L.37, H:L.94, H:T.112, H:W.113, H:L.119, H:L.120, H:T.193, H:L.197, H:L.200, H:L.200 Hydrogen bonds: H:W.31, H:G.34, H:S.205, H:N.206 Water bridges: H:F.33, H:S.35, H:H.97 Salt bridges: H:H.97, H:R.100, H:R.100 pi-Stacking: H:H.97 Metal complexes: H:H.196 HEM.23: 29 residues within 4Å: Chain S: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.84, A.87, F.90, F.91, T.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, Y.273 11 PLIP interactions: 11 interactions with chain S, Hydrophobic interactions: S:L.41, S:Q.44, S:I.45, S:A.52, S:F.90, S:L.133, S:F.183 Salt bridges: S:R.80, S:R.80 Metal complexes: S:H.83, S:H.182 HEM.24: 29 residues within 4Å: Chain S: W.31, G.34, S.35, L.37, A.38, L.41, F.90, L.94, H.97, V.98, R.100, S.106, L.109, T.112, W.113, G.116, I.117, L.119, L.120, T.123, I.189, T.193, H.196, L.197, L.200, S.205, N.206, L.301 Ligands: AFI.22 23 PLIP interactions: 23 interactions with chain S, Hydrophobic interactions: S:L.37, S:L.37, S:L.94, S:V.98, S:T.112, S:L.120, S:T.193, S:L.197, S:L.200, S:L.200 Hydrogen bonds: S:W.31, S:G.34, S:S.35, S:S.205, S:N.206 Water bridges: S:F.33, S:H.97 Salt bridges: S:H.97, S:R.100, S:R.100 pi-Stacking: S:H.97 pi-Cation interactions: S:R.100 Metal complexes: S:H.196

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

2025-07-02

Peptides

Cytochrome c1: AL
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BKM
Cytochrome b-c1 complex subunit 7: CN
Cytochrome b-c1 complex subunit 8: DO
Complex III subunit 9: EP
Cytochrome b-c1 complex subunit 6: FQ
Ubiquinol-cytochrome c reductase core protein 2: GR
Cytochrome b: HS
Ubiquinol-cytochrome c reductase core protein 1: IT
UQCRB: JU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

L
d

B
A

K
T

M
a

C
G

N
g

D
C

O
c

E
E

P
e

F
F

Q
f

G
K

R
k

H
J

S
j

I
L

T
l

J
H

U
h

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c1

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Complex III subunit 9

Cytochrome b-c1 complex subunit 6

Ubiquinol-cytochrome c reductase core protein 2

Cytochrome b

Ubiquinol-cytochrome c reductase core protein 1

UQCRB