SMTL ID : 6xkx.1

R. capsulatus CIII2CIV tripartite super-complex, conformation A (SC-1A)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-1-1-1-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: C.133, H.135, L.136, C.138, C.153, C.155, H.156, S.158 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.133, A:H.135, A:C.153, A:H.156 FES.8: 8 residues within 4Å: Chain F: C.133, H.135, L.136, C.138, C.153, C.155, H.156, S.158 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.133, F:H.135, F:C.153, F:H.156

11 x HEC: HEME C(Non-covalent)(Covalent)

HEC.2: 19 residues within 4Å: Chain B: I.59, G.62, I.63, L.65, Y.69, R.94, H.97, A.98, T.142, A.143, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, N.279, Y.297 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:I.63, B:L.65, B:L.65, B:Y.69, B:A.98, B:T.142, B:A.143, B:L.149, B:L.149, B:Y.199, B:Y.199, B:P.202 Hydrogen bonds: B:N.279 Salt bridges: B:R.94, B:R.94 Metal complexes: B:H.97, B:H.198 HEC.3: 19 residues within 4Å: Chain B: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, G.132, M.133, V.209, H.212, F.216, T.219, G.220, N.221, N.222 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.51, B:L.51, B:F.104, B:I.112, B:F.216, B:F.216 Hydrogen bonds: B:G.48, B:T.219, B:N.222 Salt bridges: B:H.111, B:R.114, B:R.125 Metal complexes: B:H.111, B:H.212 HEC.4: 15 residues within 4Å: Chain C: V.54, C.55, C.58, H.59, M.117, G.118, R.128, Y.151, Y.155, F.179, A.202, R.203, M.204, P.207, L.208 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:V.54, C:Y.155, C:F.179, C:R.203, C:R.203, C:M.204, C:P.207, C:L.208 Hydrogen bonds: C:Y.151, C:R.203 Salt bridges: C:R.128 Metal complexes: C:H.59 HEC.5: 19 residues within 4Å: Chain D: I.59, G.62, I.63, L.65, Y.69, R.94, H.97, A.98, T.142, A.143, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, N.279, Y.297 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:I.63, D:L.65, D:L.65, D:Y.69, D:A.98, D:T.142, D:A.143, D:L.149, D:L.149, D:Y.199, D:Y.199, D:P.202 Hydrogen bonds: D:N.279 Salt bridges: D:R.94, D:R.94 Metal complexes: D:H.97, D:H.198 HEC.6: 18 residues within 4Å: Chain D: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, G.132, M.133, V.209, H.212, F.216, G.220, N.221, N.222 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:I.112, D:F.216, D:F.216 Hydrogen bonds: D:G.48, D:T.219, D:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212 HEC.7: 15 residues within 4Å: Chain E: V.54, C.55, C.58, H.59, M.117, G.118, R.128, Y.151, Y.155, F.179, A.202, R.203, M.204, P.207, L.208 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:V.54, E:Y.155, E:F.179, E:R.203, E:R.203, E:M.204, E:P.207, E:L.208 Hydrogen bonds: E:Y.151, E:Y.151, E:R.203 Salt bridges: E:R.128 Metal complexes: E:H.59 HEC.9: 27 residues within 4Å: Chain G: E.177, Y.178, W.260, V.267, L.271, Y.308, H.314, H.315, S.333, L.336, S.340, T.378, G.381, P.382, M.384, S.385, N.390, H.394, T.399, H.402, V.403, G.406, A.407, N.411 Chain H: S.105 Ligands: HEC.10, CU.11 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H, Hydrophobic interactions: G:W.260, G:L.271, G:L.336, G:M.384, G:V.403 Hydrogen bonds: G:N.390, G:T.399, H:S.105 Salt bridges: G:H.315, G:H.394 pi-Stacking: G:H.264 pi-Cation interactions: G:H.315 Metal complexes: G:H.402 HEC.10: 25 residues within 4Å: Chain G: F.81, A.84, V.85, I.87, A.88, L.91, F.107, R.111, H.114, V.118, E.177, Y.178, D.397, T.399, I.400, V.403, H.404, A.407, L.408, Y.452, R.494, G.498, Y.501 Chain H: K.106 Ligands: HEC.9 22 PLIP interactions: 21 interactions with chain G, 1 interactions with chain H, Hydrophobic interactions: G:F.81, G:F.81, G:A.84, G:V.85, G:I.87, G:A.88, G:L.91, G:V.118, G:Y.178, G:I.400, G:I.400, G:V.403, G:V.403, G:A.407, G:L.408, G:Y.501 Hydrogen bonds: G:R.494 Salt bridges: G:R.111, G:R.111, H:K.106 Metal complexes: G:H.114, G:H.404 HEC.12: 20 residues within 4Å: Chain H: E.66, G.67, C.68, C.71, H.72, T.108, G.109, P.110, L.112, Y.119, W.123, H.127, L.128, V.135, S.138, V.139, M.140, P.141, Y.143 Chain I: Q.123 15 PLIP interactions: 1 interactions with chain I, 14 interactions with chain H, Hydrogen bonds: I:Q.123, H:Y.119, H:S.138 Hydrophobic interactions: H:E.66, H:L.112, H:W.123, H:L.128, H:V.135, H:V.139, H:V.139, H:M.140, H:Y.143 Salt bridges: H:H.127 pi-Cation interactions: H:H.127 Metal complexes: H:H.72 HEC.13: 21 residues within 4Å: Chain I: L.144, M.174, P.175, H.177, V.191, V.195, N.218, C.219, S.221, C.222, H.223, M.233, G.234, A.235, P.236, Y.245, I.256, R.260, G.261, G.262 Ligands: HEC.14 10 PLIP interactions: 10 interactions with chain I, Hydrophobic interactions: I:P.175, I:V.191, I:V.195, I:A.235, I:I.256, I:R.260 Hydrogen bonds: I:G.261, I:G.262 Salt bridges: I:R.260 Metal complexes: I:H.223 HEC.14: 25 residues within 4Å: Chain H: R.118, Y.119, S.120 Chain I: C.121, C.124, H.125, G.134, F.135, P.136, L.138, W.143, L.144, H.145, G.146, I.152, N.155, I.156, I.160, G.262, V.263, M.264, P.265, W.267, V.286 Ligands: HEC.13 18 PLIP interactions: 18 interactions with chain I, Hydrophobic interactions: I:F.135, I:P.136, I:L.138, I:W.143, I:W.143, I:L.144, I:I.152, I:N.155, I:I.156, I:I.160, I:W.267, I:V.286 Hydrogen bonds: I:L.144, I:H.145, I:G.146 Salt bridges: I:H.145, I:H.145 Metal complexes: I:H.125

1 x CU: COPPER (II) ION(Non-covalent)

CU.11: 4 residues within 4Å: Chain G: H.264, H.314, H.315 Ligands: HEC.9 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.264, G:H.314, G:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steimle, S. et al., Cryo-EM structures of engineered active bc 1 -cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes. Nat Commun (2021)

Release Date

2020-12-30

Peptides

Ubiquinol-cytochrome c reductase iron-sulfur subunit: AF
Cytochrome b: BD
Cytochrome c1: CE
Cytochrome c oxidase, Cbb3-type, subunit I: G
Cytochrome c oxidase, Cbb3-type, subunit II: H
Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

F
R

B
C

D
P

C
D

E
Q

G
n

H
o

I
p

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cytochrome b

Cytochrome c1

Cytochrome c oxidase, Cbb3-type, subunit I

Cytochrome c oxidase, Cbb3-type, subunit II

Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy

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