SMTL ID : 6xkw.1

R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEC.1: 27 residues within 4Å: Chain A: 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 B: S.105 Ligands: HEC.2, CU.3 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A, Hydrogen bonds: B:S.105, A:N.390, A:T.399 Hydrophobic interactions: A:W.260, A:L.271, A:L.336, A:M.384, A:V.403 Salt bridges: A:H.315, A:H.394 pi-Stacking: A:H.264 pi-Cation interactions: A:H.315 Metal complexes: A:H.402 HEC.2: 25 residues within 4Å: Chain A: 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 B: K.106 Ligands: HEC.1 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.81, A:F.81, A:A.84, A:V.85, A:I.87, A:A.88, A:L.91, A:V.118, A:Y.178, A:I.400, A:I.400, A:V.403, A:V.403, A:A.407, A:L.408, A:Y.501 Hydrogen bonds: A:R.494 Salt bridges: A:R.111, A:R.111, B:K.106 Metal complexes: A:H.114, A:H.404 HEC.4: 20 residues within 4Å: Chain B: 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 C: Q.123 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:E.66, B:L.112, B:W.123, B:L.128, B:V.135, B:V.139, B:V.139, B:M.140, B:Y.143 Hydrogen bonds: B:Y.119, B:S.138, C:Q.123 Salt bridges: B:H.127 pi-Cation interactions: B:H.127 Metal complexes: B:H.72 HEC.5: 21 residues within 4Å: Chain C: 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.6 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:P.175, C:V.191, C:V.195, C:A.235, C:I.256, C:R.260 Hydrogen bonds: C:G.261, C:G.262 Salt bridges: C:R.260 Metal complexes: C:H.223 HEC.6: 25 residues within 4Å: Chain B: R.118, Y.119, S.120 Chain C: 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.5 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.135, C:P.136, C:L.138, C:W.143, C:W.143, C:L.144, C:I.152, C:N.155, C:I.156, C:I.160, C:W.267, C:V.286 Hydrogen bonds: C:L.144, C:H.145, C:G.146 Salt bridges: C:H.145, C:H.145 Metal complexes: C:H.125 HEC.8: 19 residues within 4Å: Chain G: 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 G, Hydrophobic interactions: G:I.63, G:L.65, G:L.65, G:Y.69, G:A.98, G:T.142, G:A.143, G:L.149, G:L.149, G:Y.199, G:Y.199, G:P.202 Hydrogen bonds: G:N.279 Salt bridges: G:R.94, G:R.94 Metal complexes: G:H.97, G:H.198 HEC.9: 19 residues within 4Å: Chain G: 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 G, Hydrophobic interactions: G:L.51, G:L.51, G:F.104, G:I.112, G:F.216, G:F.216 Hydrogen bonds: G:G.48, G:T.219, G:N.222 Salt bridges: G:H.111, G:R.114, G:R.125 Metal complexes: G:H.111, G:H.212 HEC.10: 15 residues within 4Å: Chain H: 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 H, Hydrophobic interactions: H:V.54, H:Y.155, H:F.179, H:R.203, H:R.203, H:M.204, H:P.207, H:L.208 Hydrogen bonds: H:Y.151, H:R.203 Salt bridges: H:R.128 Metal complexes: H:H.59 HEC.11: 19 residues within 4Å: Chain I: 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 I, Hydrophobic interactions: I:I.63, I:L.65, I:L.65, I:Y.69, I:A.98, I:T.142, I:A.143, I:L.149, I:L.149, I:Y.199, I:Y.199, I:P.202 Hydrogen bonds: I:N.279 Salt bridges: I:R.94, I:R.94 Metal complexes: I:H.97, I:H.198 HEC.12: 18 residues within 4Å: Chain I: 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 I, Hydrophobic interactions: I:L.51, I:L.51, I:F.104, I:I.112, I:F.216, I:F.216 Hydrogen bonds: I:G.48, I:T.219, I:N.222 Salt bridges: I:H.111, I:R.114, I:R.125 Metal complexes: I:H.111, I:H.212 HEC.13: 15 residues within 4Å: Chain J: 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 J, Hydrophobic interactions: J:V.54, J:Y.155, J:F.179, J:R.203, J:R.203, J:M.204, J:P.207, J:L.208 Hydrogen bonds: J:Y.151, J:Y.151, J:R.203 Salt bridges: J:R.128 Metal complexes: J:H.59

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

CU.3: 4 residues within 4Å: Chain A: H.264, H.314, H.315 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.264, A:H.314, A:H.315

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

FES.7: 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 FES.14: 8 residues within 4Å: Chain K: C.133, H.135, L.136, C.138, C.153, C.155, H.156, S.158 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.133, K:H.135, K:C.153, K:H.156

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

Cytochrome c oxidase, Cbb3-type, subunit I: A
Cytochrome c oxidase, Cbb3-type, subunit II: B
Cbb3-type cytochrome c oxidase subunit CcoP: C
Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH: D
Cytochrome c-type cyt cy: E
Ubiquinol-cytochrome c reductase iron-sulfur subunit: FK
Cytochrome b: GI
Cytochrome c1: HJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
n

B
o

C
p

D
h

E
Y

F
E

K
R

G
C

I
P

H
D

J
Q

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase, Cbb3-type, subunit I

Cytochrome c oxidase, Cbb3-type, subunit II

Cbb3-type cytochrome c oxidase subunit CcoP

Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH

Cytochrome c-type cyt cy

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cytochrome b

Cytochrome c1

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