SMTL ID : 8k9e.1

Cryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 3.3 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: 24 residues within 4Å: Chain A: R.41, F.125, V.126, L.159, M.161, C.164, L.165, H.168, L.211, T.212, N.213, C.214, C.217, H.218 Chain B: Y.78, N.880, R.881 Chain C: W.150, H.158, M.160 Chain D: Y.82, L.84 Chain E: H.27, Y.31 14 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 1 interactions with chain E, 3 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: A:F.125, A:F.125, A:V.126, A:M.161, A:L.165, C:W.150, B:N.880, B:R.881, D:L.84 Salt bridges: A:R.41, E:H.27 Metal complexes: A:H.218 pi-Stacking: C:H.158 Hydrogen bonds: B:Y.78 HEC.2: 20 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, I.205, M.206, Q.210, L.211, V.216, C.217 Chain B: R.942, I.943, K.946 Ligands: HEC.3 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:V.126, A:I.132, A:K.136, A:I.138, A:I.138, A:W.163, A:W.163, A:I.205, A:I.205, A:V.216 Hydrogen bonds: 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 Metal complexes: A:H.133, A:H.168 HEC.3: 19 residues within 4Å: Chain A: H.70, V.73, F.78, A.79, K.118, Y.120, D.121, L.122, F.128, H.130, H.133, I.138, G.139, C.140, C.143, H.144, W.163 Ligands: HEC.2, HEC.4 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:H.70, A:V.73, A:A.79, A:Y.120, A:F.128, A:F.128, A:I.138, A:W.163 Hydrogen bonds: A:A.79, 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: 21 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, K.118, V.119, Y.120, C.140, H.144, V.147, V.153, M.184 Ligands: HEC.3, HEC.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.53, A:V.59, A:I.64, A:P.82, A:W.116, A:V.147, A:V.147, A:V.153 Hydrogen bonds: A:V.119, A:Y.120 Salt bridges: A:H.55, A:K.118 Metal complexes: A:H.55, A:H.70 HEC.5: 17 residues within 4Å: Chain A: A.52, 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.101 Chain E: V.117, R.120 Ligands: HEC.4 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: A:L.57, A:V.62, A:I.64, A:Y.68, A:I.94, A:L.101, E:V.117, E:R.120 Salt bridges: A:K.95, A:K.95, E:R.120 pi-Stacking: A:F.53 Metal complexes: A:H.58, A:H.91 HEC.12: 23 residues within 4Å: Chain A: T.89 Chain E: Y.102, C.103, V.105, 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.177, I.181 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:I.123, E:F.128, E:F.141, E:V.144, E:V.144, E:I.145, E:I.145, E:V.149, E:I.177, E:I.181 Hydrogen bonds: E:S.161 Salt bridges: E:R.132, E:H.140 pi-Stacking: E:H.107 Metal complexes: E:H.107

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

SF4.6: 11 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, T.974 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.794, B:C.797, B:C.800, B:C.972 SF4.7: 12 residues within 4Å: Chain B: M.787, C.804, N.808, W.826, I.827, 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: 13 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 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(Non-covalent)

F3S.9: 13 residues within 4Å: Chain B: C.862, V.864, A.866, M.877, C.882, V.883, G.884, T.885, K.886, Y.887, C.888, R.897, M.928 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.862, B:C.882, B:C.888

2 x EL6: [(2S)-2-octadecanoyloxypropyl] octadecanoate(Non-covalent)(Covalent)

EL6.10: 2 residues within 4Å: Chain B: C.76 Ligands: EL6.13 No protein-ligand interaction detected (PLIP) EL6.13: 6 residues within 4Å: Chain A: G.27, L.31, Y.34, F.35 Chain E: C.26 Ligands: EL6.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.31, A:F.35

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

JLQ.11: 16 residues within 4Å: Chain C: Y.18, Q.113, W.115, V.306, K.309, V.310, T.313, I.317 Chain F: F.64, V.67, L.70, T.71, G.72, M.227, G.231 Ligands: JL3.14 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:Q.113, C:W.115, C:V.310, C:V.310, C:T.313, F:F.64, F:V.67 Hydrogen bonds: C:Y.18, C:Y.18 Salt bridges: C:K.309, C:K.309

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

JL3.14: 15 residues within 4Å: Chain C: I.107, L.110, L.111, N.112, Q.113 Chain F: T.71, G.72, G.73, A.74, W.75, K.258, D.262, K.265, A.269 Ligands: JLQ.11 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain C Hydrophobic interactions: F:W.75, F:K.265, F:A.269, C:I.107, C:L.111, C:L.111 Hydrogen bonds: F:T.71, F:A.74, C:N.112, C:Q.113 Salt bridges: F:K.258, F:K.265

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

JM9.15: 23 residues within 4Å: Chain C: L.110, M.229, L.233, G.236, L.237, P.240 Chain D: P.56, V.59, L.60, G.63, A.67, F.104, G.107, I.108 Chain F: K.265, F.268, V.272, Y.276, F.321, L.325, F.326, R.327, K.330 21 PLIP interactions: 9 interactions with chain F, 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: F:K.265, F:F.268, F:V.272, F:V.272, F:Y.276, F:Y.276, F:F.321, D:P.56, D:V.59, D:L.60, D:L.60, D:A.67, D:F.104, D:F.104, D:F.104, D:I.108, C:L.110, C:L.233, C:P.240 Hydrogen bonds: F:R.327 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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