SMTL ID : 8k9f.1

Cryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 2.9 angstrom

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(Non-covalent)(Covalent)

HEC.1: 26 residues within 4Å: Chain A: R.41, L.122, 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, H.158, M.160 Chain D: Y.82, L.84 Chain E: H.27, Y.31 Ligands: HEC.2 13 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E, 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain D, Hydrophobic interactions: A:L.122, A:M.161, A:L.165, C:W.150, B:R.881, D:Y.82, D:L.84 Hydrogen bonds: A:L.159, B:Y.78 Salt bridges: A:R.41, E:H.27, C:H.158 Metal complexes: A:H.218 HEC.2: 22 residues within 4Å: Chain A: V.126, F.128, I.132, H.133, K.136, I.138, W.163, C.164, C.167, H.168, G.204, I.205, M.206, Q.210, L.211, V.216, C.217 Chain B: R.942, I.943, K.946 Ligands: HEC.1, HEC.3 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:V.126, A:I.132, A:I.138, A:I.138, A:W.163, A:W.163, A:I.205, A:L.211, A:V.216, B:I.943 Hydrogen bonds: A:G.204, A:M.206, A:Q.210 Salt bridges: A:K.136, B:R.942, B:K.946, B:K.946 pi-Stacking: A:F.128, A:H.133 Metal complexes: A:H.133 HEC.3: 23 residues within 4Å: Chain A: C.66, H.70, V.73, F.78, A.79, I.81, K.118, Y.120, D.121, L.122, F.128, H.130, V.134, I.138, G.139, C.140, C.143, H.144, L.159, W.163, V.181 Ligands: HEC.2, HEC.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.73, A:F.78, A:A.79, A:I.81, A:Y.120, A:F.128, A:F.128, A:V.134, A:I.138, A:L.159, A:W.163, A:V.181 Hydrogen bonds: 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, I.81, P.82, W.116, V.117, K.118, V.119, Y.120, C.140, V.147, V.153, M.184 Ligands: HEC.3, HEC.5 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.53, A:V.59, A:I.64, A:P.82, A:W.116, A:W.116, A:W.116, A:V.147, A:V.153 Hydrogen bonds: A:V.119, A:Y.120, A:Y.120 Salt bridges: A:K.118 pi-Stacking: A:F.53 Metal complexes: A:H.70 HEC.5: 20 residues within 4Å: Chain A: V.51, F.53, L.57, H.58, V.62, I.64, Y.68, T.86, C.87, C.90, H.91, I.94, K.95, L.100, L.101, V.104, W.116 Chain E: V.117, R.120 Ligands: HEC.4 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:V.51, A:F.53, A:L.57, A:V.62, A:I.64, A:Y.68, A:I.94, A:K.95, A:L.100, A:L.101, A:V.104, A:W.116, E:R.120 Hydrogen bonds: A:K.95 Salt bridges: A:H.91, A:K.95, A:K.95 pi-Stacking: A:F.53, A:H.91, A:H.91 Metal complexes: A:H.58 HEC.12: 23 residues within 4Å: Chain A: T.89 Chain E: Y.102, C.103, V.105, C.106, H.107, I.123, V.124, P.125, A.126, F.128, R.132, L.133, F.141, V.144, I.145, V.149, S.161, M.162, Y.165, I.169, I.177, I.181 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:I.123, E:P.125, E:F.128, E:L.133, E:F.141, E:V.144, E:I.145, E:M.162, E:I.169, E:I.177, E:I.181 Hydrogen bonds: E:S.161 Salt bridges: E:R.132 Metal complexes: E:H.107

3 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.6: 12 residues within 4Å: Chain B: C.794, I.795, G.796, C.797, N.798, A.799, C.800, P.847, C.972, P.973, T.974, A.976 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:C.794, B:C.797, B:C.797, B:C.800, B:C.972, B:C.972 SF4.7: 10 residues within 4Å: Chain B: C.804, N.808, W.826, I.827, N.849, C.931, Y.933, C.934, T.966, C.968 7 PLIP interactions: 7 interactions with chain B, Metal complexes: B:C.804, B:C.804, B:C.931, B:C.931, B:C.934, B:C.968, B:C.968 SF4.8: 11 residues within 4Å: Chain B: C.850, M.851, Q.852, C.853, A.856, C.858, N.875, C.892, Y.894, V.896, K.930 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.850, B:C.853, B:C.858, B:C.858, B:C.892

1 x F3S: FE3-S4 CLUSTER(Covalent)

F3S.9: 11 residues within 4Å: Chain B: C.862, P.863, V.864, M.877, C.882, V.883, G.884, T.885, K.886, Y.887, C.888 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.862, B:C.882, B:C.888

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 6 residues within 4Å: Chain A: D.121, L.122 Chain B: Q.79, Q.82 Chain E: Y.31, D.32 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Metal complexes: A:D.121, E:D.32

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

JLQ.11: 26 residues within 4Å: Chain C: Y.18, Q.113, W.115, P.268, V.271, A.272, H.302, V.306, K.309, V.310, T.313, T.314, I.317 Chain F: G.60, G.63, F.64, V.67, L.70, T.71, V.195, V.199, M.227, G.231, F.270, N.401 Ligands: JL3.13 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain F Hydrophobic interactions: C:W.115, C:V.271, C:A.272, C:V.310, C:V.310, C:T.314, F:F.64, F:L.70, F:V.195, F:V.199, F:F.270 Hydrogen bonds: C:Y.18, F:N.401 Salt bridges: C:H.302, C:K.309, C:K.309

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

JL3.13: 18 residues within 4Å: Chain C: H.99, I.107, L.111, N.112, V.243, I.317 Chain F: V.67, T.71, G.73, A.74, W.75, K.258, D.262, K.265, L.266, A.269, Q.404 Ligands: JLQ.11 17 PLIP interactions: 11 interactions with chain F, 6 interactions with chain C Hydrophobic interactions: F:V.67, F:T.71, F:W.75, F:K.265, F:L.266, F:L.266, F:A.269, C:I.107, C:L.111, C:L.111, C:V.243, C:I.317 Hydrogen bonds: F:T.71, F:A.74, F:D.262, C:N.112 Salt bridges: F:K.258

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

JM9.14: 23 residues within 4Å: Chain C: L.110, L.233, G.236, L.237, P.240, V.243 Chain D: P.56, L.60, G.63, L.64, F.104, G.107 Chain F: H.261, F.268, V.272, L.273, T.275, Y.276, F.321, L.325, F.326, R.327, K.330 21 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D, 13 interactions with chain F Hydrophobic interactions: C:L.110, C:L.233, C:L.237, C:P.240, C:V.243, D:L.60, D:F.104, D:F.104, F:F.268, F:V.272, F:L.273, F:T.275, F:Y.276, F:F.321, F:L.325, F:F.326, F:F.326 Hydrogen bonds: F:R.327 Salt bridges: F:H.261, F:K.265, 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
hypothetical 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

hypothetical protein

unknown

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