SMTL ID : 9f61.1

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, H.284, H.285, T.303, I.306, A.307, T.310, G.311, I.314, T.343, 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, I.221 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.231, A:V.238, A:V.238, A:T.310, A:I.314, A:T.343, A:V.350, A:L.352, A:F.371, A:F.371, A:V.374, A:L.375, B:P.218, B:I.221 Hydrogen bonds: A:Y.239, A:D.358 Salt bridges: A:H.362, A:R.432 pi-Cation interactions: A:H.235, A:H.235 Metal complexes: A:H.370 HEA.2: 32 residues within 4Å: Chain A: L.17, F.21, 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, V.368, F.371, H.372, S.376, V.380, L.411, V.415, T.418, F.419, Q.422, R.432, R.433, M.434, A.452, V.459 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:F.21, A:I.34, A:R.35, A:M.64, A:L.65, A:V.69, A:V.368, A:F.371, A:F.371, A:V.380, A:L.411, A:T.418, 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.433, A:M.434 Salt bridges: A:R.432, 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.362, A:D.363, C:E.122

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: 14 residues within 4Å: Chain A: H.228, W.282, L.291, D.292, T.295 Chain D: W.226, L.229, H.230, M.233 Chain L: M.28, C.29, V.32, P.37, E.38 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: L:V.32, L:P.37, A:D.292, D:M.233 Salt bridges: A:H.228, D:H.230

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

PGT.6: 17 residues within 4Å: Chain A: A.92, F.93, P.94, R.95, L.96, I.99 Chain D: H.135, L.137, A.182, W.185, W.186, C.189, E.192, H.198, F.206, F.213 Ligands: 3PH.9 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:A.182, D:W.185, D:W.185, D:W.185, D:F.213, A:I.99 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 B: W.254 Chain C: H.85, 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: 18 residues within 4Å: Chain A: V.204, L.207 Chain D: M.157, Y.305, N.306, T.308, F.310, T.311, I.312, F.322, V.323, G.326, F.327 Chain G: W.98, G.102, L.103, F.104, E.105 8 PLIP interactions: 2 interactions with chain G, 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: G:W.98, G:L.103, D:I.312, D:F.327, A:V.204, A:L.207 Hydrogen bonds: D:T.308, D:I.312 PTY.10: 10 residues within 4Å: Chain A: T.348, F.420, H.423 Chain B: L.151, L.152, F.172 Chain F: L.46, A.49, W.50, W.53 9 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: F:W.50, F:W.50, A:T.348, A:F.420, B:L.152, B:F.172, B:F.172, B:F.172 Hydrogen bonds: B:L.152

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

3PH.9: 18 residues within 4Å: Chain D: W.186, C.189, A.190, G.193, H.198, F.206, M.210, L.334, L.337, Y.338, A.341, M.345, A.352, G.353, A.354, A.355, Y.362 Ligands: PGT.6 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.186, D:W.186, D:W.186, D:L.334, D:L.334, D:L.337, D:Y.338, D:Y.338, D:Y.338, D:A.341 Hydrogen bonds: D:A.352, D:A.352, D:A.354, D:A.355 3PH.11: 6 residues within 4Å: Chain A: A.463 Chain I: Y.74, A.75, G.78, A.79, Y.81 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:A.79, I:Y.81, A:A.463

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
3A

B
3B

C
3C

D
3D

E
3E

F
3F

G
3G

H
3H

I
3I

J
3J

K
3K

L
3L

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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