SMTL ID : 8dh6.1

Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.39, A.42, G.44, Q.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.39, A:E.39, A:A.42, A:G.44

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: H.368 Chain B: E.208 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.368, B:E.208

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

CU.3: 3 residues within 4Å: Chain A: H.241, H.290, H.291 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.241, A:H.241, A:H.290, A:H.291 CU.10: 6 residues within 4Å: Chain B: H.171, C.206, E.208, C.210, H.214, M.217 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.206, B:C.210

2 x HEA: HEME-A(Covalent)(Non-covalent)

HEA.4: 34 residues within 4Å: Chain A: F.19, I.23, G.26, T.30, S.33, R.37, F.55, V.59, H.62, A.63, M.66, I.67, L.70, V.71, G.126, W.127, Y.371, F.377, H.378, L.381, S.382, I.386, L.389, F.390, I.424, F.425, M.428, R.438, R.439, I.440, S.458, A.461, L.465, F.468 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:F.19, A:I.23, A:T.30, A:V.59, A:A.63, A:M.66, A:I.67, A:V.71, A:F.377, A:L.381, A:I.386, A:I.386, A:L.389, A:F.390, A:F.390, A:I.424, A:A.461, A:L.465, A:L.465, A:F.468 Hydrogen bonds: A:R.37, A:W.127, A:S.382, A:R.439, A:I.440 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:H.378, A:F.425 Metal complexes: A:H.62, A:H.378 HEA.5: 33 residues within 4Å: Chain A: W.127, T.128, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, I.312, A.313, T.316, G.317, F.348, T.349, G.352, L.353, G.355, V.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.35, P.74, I.77, L.78 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.237, A:V.244, A:I.248, A:T.309, A:T.316, A:F.348, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.35, B:I.77, B:L.78 Hydrogen bonds: A:W.127, A:Y.245, A:Y.245 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376

10 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.6: 15 residues within 4Å: Chain A: F.95, P.96, R.97, I.98, L.160 Chain C: H.15, V.17, V.26, S.62, W.65, F.66, I.87, G.90, F.91 Ligands: PEF.12 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:R.97, A:I.98 Salt bridges: A:R.97 Hydrophobic interactions: C:V.26, C:W.65, C:W.65, C:W.65, C:F.66 PEF.7: 19 residues within 4Å: Chain A: L.34, I.35, L.38, Y.47, L.48, F.459, T.462, L.463, F.466 Chain E: F.85, L.89, A.96, G.97, Q.99 Chain H: F.38, C.41, Y.42, L.45, F.51 14 PLIP interactions: 10 interactions with chain A, 2 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: A:L.34, A:Y.47, A:F.459, A:L.463, A:L.463, A:L.463, A:F.466, A:F.466, A:F.466, E:F.85, E:L.89, H:F.38, H:F.51 Hydrogen bonds: A:Y.47 PEF.8: 19 residues within 4Å: Chain A: F.268, F.321, A.325 Chain B: L.38, M.42, I.60, H.62, G.63, Q.64, I.66, I.69, W.70, F.73 Chain I: K.10, V.13, I.14, I.17, V.18, F.21 20 PLIP interactions: 9 interactions with chain B, 9 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: B:L.38, B:I.66, B:I.66, B:I.69, B:W.70, B:F.73, I:K.10, I:V.13, I:I.14, I:I.17, I:I.17, I:F.21, I:F.21, I:F.21, I:F.21, A:F.321, A:A.325 Hydrogen bonds: B:H.62, B:G.63, B:Q.64 PEF.9: 6 residues within 4Å: Chain A: F.426, W.450 Chain B: Y.6, C.8 Chain E: Q.131 Ligands: PEF.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.426 PEF.11: 16 residues within 4Å: Chain A: L.353, T.354, F.426, H.429, F.430, I.433 Chain B: T.4, Y.6, A.7, C.8, Y.9, L.32, L.36 Chain I: W.31, F.35 Ligands: PEF.9 12 PLIP interactions: 6 interactions with chain A, 3 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: A:L.353, A:T.354, A:F.426, A:F.430, A:F.430, A:I.433, I:W.31, I:W.31, I:F.35, B:L.32 Hydrogen bonds: B:P.5, B:C.8 PEF.12: 18 residues within 4Å: Chain C: F.66, I.69, V.70, A.73, T.74, H.79, I.87, M.218, M.222, V.225, R.229, H.234, H.239, H.240, V.241, G.242 Ligands: PEF.6, PEF.16 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:F.66, C:F.66, C:I.87, C:V.225 Hydrogen bonds: C:V.241, C:G.242 Salt bridges: C:H.79, C:R.229, C:R.229, C:H.239 PEF.13: 12 residues within 4Å: Chain A: T.208, F.216 Chain C: I.101, Y.189, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.214 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:I.101, C:I.196, C:L.214, A:T.208, A:F.216, A:F.216, A:F.216 Hydrogen bonds: C:A.192, C:F.194, C:I.196 PEF.15: 12 residues within 4Å: Chain A: L.334, L.339, Q.411, F.414, W.415, F.418, I.419 Chain B: S.40 Chain E: L.67, S.72, I.75, V.79 12 PLIP interactions: 2 interactions with chain E, 10 interactions with chain A Hydrophobic interactions: E:I.75, E:V.79, A:L.334, A:L.334, A:L.339, A:F.414, A:W.415, A:W.415, A:W.415, A:F.418, A:I.419, A:I.419 PEF.16: 15 residues within 4Å: Chain C: I.63, F.66, R.67, Y.75, V.179, A.220, A.221, V.225, W.228, N.232, H.234 Chain G: H.22, R.24, Y.28 Ligands: PEF.12 14 PLIP interactions: 5 interactions with chain G, 9 interactions with chain C Hydrophobic interactions: G:Y.28, C:I.63, C:R.67, C:R.67, C:V.179, C:A.220, C:W.228, C:W.228 Hydrogen bonds: G:R.24, G:Y.28, C:Y.75 Salt bridges: G:H.22, G:R.24, C:H.234 PEF.17: 15 residues within 4Å: Chain A: V.16, F.19, M.20, Y.393, I.400, L.401 Chain H: F.13, K.14, R.18, K.19, T.20, Y.22, S.25, H.26, F.30 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain H Hydrophobic interactions: A:V.16, A:F.19, A:F.19, A:Y.393, A:I.400, A:L.401, H:F.13, H:F.13, H:R.18, H:K.19, H:T.20, H:F.30 Hydrogen bonds: H:S.25 Salt bridges: H:R.18

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain D: C.86, H.94, C.109, C.112 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.86, D:H.94, D:C.109, D:C.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoy, A.S. et al., Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs. To Be Published

Release Date

2022-07-20

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 6, mitochondrial: F
Cytochrome c oxidase subunit 7, mitochondrial: G
Cytochrome c oxidase subunit 8, mitochondrial: H
Cytochrome c oxidase subunit 9, mitochondrial: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
d

E
e

F
f

G
g

H
h

I
i

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7, mitochondrial

Cytochrome c oxidase subunit 8, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

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