SMTL ID : 8x2j.1

Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: R.41, L.122, F.125, V.126, L.159, Y.160, M.161, C.164, L.165, H.168, T.212, N.213, C.214, C.217, H.218 Chain B: Y.78, A.865, N.880, R.881 Chain C: W.150, T.157, H.158, M.160 Chain D: Y.82 Chain E: H.27, Y.31 Ligands: HEC.2 15 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 2 interactions with chain E, 7 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: C:W.150, B:R.881, B:R.881, A:L.122, A:F.125, A:F.125, A:V.126, A:M.161, D:Y.82 Hydrogen bonds: C:T.157, E:Y.31 pi-Stacking: C:H.158 Salt bridges: E:H.27, A:R.41 Metal complexes: A:H.218 HEC.2: 22 residues within 4Å: Chain A: L.122, V.126, Y.127, F.128, I.132, H.133, K.136, I.138, W.163, C.164, C.167, H.168, I.205, M.206, L.211, V.216, C.217 Chain B: R.942, I.943, K.946 Ligands: HEC.1, HEC.3 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:L.122, A:V.126, A:I.132, A:K.136, A:I.138, A:I.138, A:W.163, A:W.163, A:L.211, A:V.216, B:I.943 Hydrogen bonds: A:M.206 Salt bridges: A:K.136, B:R.942, B:K.946, B:K.946 pi-Stacking: A:F.128 Metal complexes: A:H.168 HEC.3: 22 residues within 4Å: Chain A: H.70, V.73, F.78, A.79, I.81, K.118, Y.120, D.121, L.122, F.128, H.130, H.133, V.134, I.138, G.139, C.140, C.143, H.144, L.159, Y.182 Ligands: HEC.2, HEC.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.78, A:A.79, A:I.81, A:K.118, A:L.122, A:F.128, A:F.128, A:V.134, A:I.138, A:L.159, A:Y.182 Hydrogen bonds: A:A.79, A:Y.120, A:L.122 Salt bridges: A:K.118, A:K.118, A:H.130 Metal complexes: A:H.130, A:H.144 HEC.4: 22 residues within 4Å: Chain A: Q.49, F.53, H.55, V.59, I.64, D.65, C.66, C.69, H.70, P.82, W.116, V.117, K.118, V.119, Y.120, C.140, H.144, V.147, V.153, M.184 Ligands: HEC.3, HEC.5 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.53, A:F.53, A:V.59, A:V.59, A:I.64, A:I.64, A:P.82, A:W.116, A:W.116, A:Y.120, A:V.147, A:V.147, A:V.153 Hydrogen bonds: A:V.119, A:Y.120, A:Y.120 Salt bridges: A:H.55 Metal complexes: A:H.55, A:H.70 HEC.5: 18 residues within 4Å: Chain A: F.53, L.57, H.58, I.64, Y.68, T.86, C.87, C.90, H.91, I.94, K.95, L.100, L.101, V.104 Chain E: V.105, V.117, R.120 Ligands: HEC.4 14 PLIP interactions: 3 interactions with chain E, 11 interactions with chain A, Hydrophobic interactions: E:V.105, E:V.117, A:F.53, A:Y.68, A:I.94, A:L.100, A:L.101, A:L.101, A:V.104 Salt bridges: E:R.120, A:K.95 pi-Stacking: A:F.53 Metal complexes: A:H.58, A:H.91 HEC.14: 22 residues within 4Å: Chain A: C.90 Chain E: Y.102, C.103, C.106, H.107, I.123, P.125, A.126, F.128, R.132, L.133, H.140, F.141, V.144, I.145, V.149, Y.150, S.161, M.162, Y.165, I.169, I.177 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:I.123, E:A.126, E:F.128, E:F.141, E:V.144, E:V.144, E:I.145, E:I.145, E:V.149, E:M.162, E:Y.165, E:I.169, E:I.177 Hydrogen bonds: E:Y.150 Salt bridges: E:R.132, E:H.140 Metal complexes: E:H.107

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 13 residues within 4Å: Chain B: C.794, I.795, G.796, C.797, N.798, A.799, C.800, I.829, P.847, C.972, P.973, T.974, I.977 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.794, B:C.797, B:C.800, B:C.972 SF4.7: 13 residues within 4Å: Chain B: M.787, C.804, N.808, W.826, I.827, N.849, C.931, T.932, Y.933, C.934, T.966, A.967, C.968 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.804, B:C.931, B:C.934, B:C.968 SF4.8: 14 residues within 4Å: Chain B: C.850, M.851, Q.852, C.853, A.856, P.857, C.858, N.875, C.892, P.893, Y.894, V.896, R.897, K.930 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.850, B:C.853, B:C.858, B:C.892

1 x F3S: FE3-S4 CLUSTER(Covalent)

F3S.9: 14 residues within 4Å: Chain B: V.861, C.862, P.863, V.864, T.867, M.877, C.882, V.883, G.884, T.885, K.886, Y.887, C.888, M.928 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.862, B:C.882, B:C.888

1 x JLQ: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate(Covalent)

JLQ.10: 23 residues within 4Å: Chain C: Y.18, L.111, Q.113, W.115, V.271, H.302, V.306, K.309, T.313, T.314, I.317 Chain F: F.64, V.67, L.70, T.71, G.72, V.195, F.198, V.199, M.227, G.231, N.401 Ligands: JL3.12 18 PLIP interactions: 9 interactions with chain C, 9 interactions with chain F Hydrophobic interactions: C:L.111, C:W.115, C:V.271, C:T.314, F:F.64, F:V.67, F:T.71, F:V.195, F:V.195, F:F.198, F:F.198, F:V.199 Hydrogen bonds: C:Y.18, C:Y.18, F:N.401 Salt bridges: C:H.302, C:K.309, C:K.309

1 x HQO: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE(Non-covalent)

HQO.11: 15 residues within 4Å: Chain B: T.885 Chain C: W.84, I.88, F.91, P.138, H.141, L.142, L.151, I.152, L.168, D.171, V.172, I.175, S.176, D.252 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.84, C:I.88, C:F.91, C:P.138, C:L.151, C:I.152, C:L.168, C:D.171, C:V.172, C:I.175 Hydrogen bonds: C:D.171

1 x JL3: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate(Covalent)

JL3.12: 22 residues within 4Å: Chain C: I.107, L.110, L.111, N.112, T.239, V.243, K.460 Chain F: V.67, T.71, G.72, G.73, A.74, W.75, D.262, K.265, L.266, A.269, F.270, L.273, Q.404 Ligands: JLQ.10, JM9.13 18 PLIP interactions: 9 interactions with chain C, 9 interactions with chain F Hydrophobic interactions: C:I.107, C:L.110, C:L.111, C:L.111, C:T.239, C:V.243, F:V.67, F:W.75, F:K.265, F:L.266, F:A.269, F:F.270, F:L.273 Hydrogen bonds: C:N.112, C:K.460, C:K.460, F:T.71, F:A.74

1 x JM9: 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate(Covalent)

JM9.13: 24 residues within 4Å: Chain C: L.110, M.229, I.232, L.233, G.236, L.237, T.239, P.240, V.243, S.244 Chain D: P.56, V.59, F.104 Chain F: K.265, F.268, A.269, V.272, T.275, Y.276, F.317, F.321, L.325, K.330 Ligands: JL3.12 20 PLIP interactions: 4 interactions with chain C, 11 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: C:L.233, C:T.239, C:P.240, C:V.243, F:F.268, F:F.268, F:F.268, F:V.272, F:T.275, F:Y.276, F:Y.276, F:F.317, F:F.321, F:L.325, D:P.56, D:V.59, D:F.104, D:F.104, D:F.104 Salt bridges: F:K.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xin, J. et al., Cryo-EM structure of HQNO-bound Alternative Complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus. Plant Cell (2024)

Release Date

2024-03-06

Peptides

Cytochrome c7-like domain-containing protein: A
Fe-S-cluster-containing hydrogenase components 1-like protein: B
Polysulphide reductase NrfD: C
Quinol:cytochrome c oxidoreductase membrane protein: D
Cytochrome c domain-containing protein: E
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2: F
Uncharacterized protein: G
unknown: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c7-like domain-containing protein

Fe-S-cluster-containing hydrogenase components 1-like protein

Polysulphide reductase NrfD

Quinol:cytochrome c oxidoreductase membrane protein

Cytochrome c domain-containing protein

Quinol:cytochrome c oxidoreductase quinone-binding subunit 2

Uncharacterized protein

unknown

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