SMTL ID : 9f60.1

Structure of the Chlamydomonas reinhardtii respiratory complex IV from respiratory supercomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEA.1: 29 residues within 4Å: Chain A: W.125, W.231, V.238, Y.239, I.242, H.284, H.285, T.303, I.306, A.307, T.310, G.311, I.314, F.342, G.346, G.349, V.350, L.352, A.353, D.358, H.362, V.367, H.370, F.371, V.374, L.375, R.432 Chain B: V.178, P.218 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.231, A:V.238, A:V.238, A:I.242, A:I.314, A:F.342, A:V.350, A:L.352, A:F.371, A:F.371, A:V.374, A:L.375, B:V.178, B:V.178, B:P.218 Hydrogen bonds: A:Y.239, A:D.358 Salt bridges: A:H.362, A:R.432 Metal complexes: A:H.370 HEA.2: 35 residues within 4Å: Chain A: L.17, A.20, F.21, G.24, T.28, S.31, I.34, R.35, Y.53, I.57, H.60, G.61, M.64, L.65, M.68, V.69, G.124, W.125, Y.365, F.371, H.372, L.375, S.376, V.380, I.383, F.384, V.387, L.411, T.418, F.419, Q.422, R.432, R.433, A.452, V.459 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:A.20, A:F.21, A:L.65, A:V.69, A:L.375, A:V.380, A:I.383, A:F.384, A:V.387, A:L.411, A:T.418, A:F.419, A:F.419, A:A.452, A:V.459 Hydrogen bonds: A:R.35, A:Y.53, A:Y.53, A:I.57, A:W.125, A:S.376, A:S.376, A:Q.422, A:R.432, A:R.433 Salt bridges: A:R.433 pi-Stacking: A:F.371, A:H.372, A:F.419 Metal complexes: A:H.372

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

CU.3: 3 residues within 4Å: Chain A: H.235, H.284, H.285 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.235, A:H.284, A:H.285

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: H.362, D.363 Chain C: E.122 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.362, A:D.363

1 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.5: 15 residues within 4Å: Chain A: H.228, W.282, L.291, D.292, T.295, F.299 Chain D: W.226, H.230, M.233, S.234 Chain L: F.25, M.28, C.29, V.32, E.38 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:M.233 Salt bridges: D:H.230, A:H.228, A:H.228 Hydrogen bonds: A:D.292

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.6: 14 residues within 4Å: Chain A: A.92, F.93, P.94, R.95, L.96 Chain D: H.135, A.182, W.185, W.186, C.189, E.192, H.198, F.206 Ligands: 3PH.9 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:A.182, D:W.185 Hydrogen bonds: A:F.93, A:R.95, A:R.95, A:L.96 Salt bridges: A:R.95

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.7: 7 residues within 4Å: Chain C: H.85, S.86, C.120, E.122, C.124, H.128, M.131 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.120, C:E.122, C:C.124, C:H.128

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.8: 16 residues within 4Å: Chain A: L.145, H.148, L.207 Chain D: M.157, Y.305, T.308, F.310, T.311, I.312, F.322, G.326, F.327 Chain G: W.98, G.102, L.103, F.104 7 PLIP interactions: 2 interactions with chain G, 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: G:W.98, D:I.312, D:F.327, A:L.145, A:L.207 Hydrogen bonds: G:L.103, D:I.312 PTY.10: 12 residues within 4Å: Chain A: L.344, V.347, T.348, H.423, F.424 Chain B: Q.150, L.151, L.152, F.172 Chain F: L.46, W.50, W.53 14 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B, 2 interactions with chain J, 1 interactions with chain F Hydrophobic interactions: A:L.344, A:V.347, A:T.348, A:H.423, A:F.424, B:L.152, B:F.172, B:F.172, F:L.46 Hydrogen bonds: B:Q.150, B:L.151, B:L.152, J:T.89, J:T.89

2 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.9: 16 residues within 4Å: Chain D: W.186, C.189, A.190, G.193, H.198, F.206, M.210, F.213, L.334, L.337, Y.338, A.341, M.345, A.352, A.354 Ligands: PGT.6 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.186, D:W.186, D:W.186, D:F.213, D:L.334, D:L.334, D:L.337, D:A.341 Hydrogen bonds: D:A.354, D:A.355 Salt bridges: D:H.198 3PH.11: 6 residues within 4Å: Chain A: A.463, T.464 Chain I: Y.74, A.79, Y.81, A.82 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:A.463, I:Y.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waltz, F. et al., In-cell architecture of the mitochondrial respiratory chain. Science (2025)

Release Date

2025-03-12

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase polypeptide II: B
cytochrome-c oxidase: C
Cytochrome c oxidase subunit 3: D
Cox5b: E
Cox5c: F
Cox6a: G
Cox6b: H
Cox7c: I
Cytochrome c oxidase subunit: J
Cox7a: K
CoxIn: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2A

B
2B

C
2C

D
2D

E
2E

F
2F

G
2G

H
2H

I
2I

J
2J

K
2K

L
2L

Membrane

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

Cytochrome c oxidase polypeptide II

cytochrome-c oxidase

Cytochrome c oxidase subunit 3

Cox5b

Cox5c

Cox6a

Cox6b

Cox7c

Cytochrome c oxidase subunit

Cox7a

CoxIn

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