SMTL ID : 8ugl.1

High resolution in-situ structure of complex IV in respiratory supercomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

15 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.1: 16 residues within 4Å: Chain A: F.2, V.3, L.7, Y.8, W.103, P.106, P.107, L.110 Chain C: L.18, L.22, L.25 Chain J: Y.53, M.57, L.61 Ligands: PGV.26, PGV.28 14 PLIP interactions: 4 interactions with chain C, 8 interactions with chain A, 2 interactions with chain J Hydrophobic interactions: C:L.18, C:L.18, C:L.22, C:L.25, A:F.2, A:V.3, A:V.3, A:W.103, A:P.106, A:P.107, A:L.110, J:L.61, J:L.61 Hydrogen bonds: A:V.3 PGV.2: 21 residues within 4Å: Chain A: K.172, S.177, Q.178, Y.179, W.186, L.189, I.190, V.193, L.197, W.275, M.278, S.279, G.281, F.282, F.285 Chain N: M.1, Q.4, I.5, F.19, I.22 Ligands: CDL.18 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain N Hydrophobic interactions: A:L.189, A:I.190, A:V.193, A:V.193, A:L.197, A:W.275, A:M.278, A:F.282, A:F.282, A:F.285, N:I.5, N:F.19, N:F.19, N:I.22 Hydrogen bonds: A:K.172, A:S.177, A:Q.178, N:Q.4 PGV.3: 25 residues within 4Å: Chain A: I.229, H.233, F.237, F.282, I.286, W.288, V.295, G.296, M.297, D.298, T.301, Y.304, F.305 Chain B: R.178 Chain C: V.91, T.95, W.99 Chain N: G.26, A.29, Y.32, V.33, L.36, N.40 Ligands: PGV.16, CDL.18 18 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B, 3 interactions with chain N, 3 interactions with chain C Hydrophobic interactions: A:F.237, A:F.237, A:F.282, A:I.286, A:W.288, A:Y.304, N:A.29, N:Y.32, C:V.91, C:T.95, C:W.99 Hydrogen bonds: A:D.298, A:D.298, A:T.301, B:R.178, B:R.178, N:N.40 Salt bridges: A:H.233 PGV.9: 14 residues within 4Å: Chain A: W.334, L.342, G.343, F.346, F.414, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, T.48, K.49 Ligands: CDL.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.334, B:K.49 PGV.13: 30 residues within 4Å: Chain A: A.93, F.94, P.95, R.96, M.97, M.100, L.152, V.155, I.158, L.159, P.200 Chain C: H.9, V.11, A.24, T.28, L.31, N.50, M.54, W.57, W.58, I.61, E.64, H.71, G.82, M.83, F.86, F.93 Ligands: PGV.15, PGV.19, PEK.24 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.152, A:V.155, A:I.158, A:L.159, A:P.200, C:A.24, C:T.28, C:L.31, C:W.57, C:W.57, C:W.57, C:F.86, C:F.86, C:F.93 Hydrogen bonds: A:A.93, A:R.96, A:M.97, C:H.71 Salt bridges: A:R.96 PGV.14: 11 residues within 4Å: Chain C: R.156, K.157, Q.161, S.164, I.165, I.167, A.168, L.219 Chain J: L.22 Ligands: PGV.22, PEK.23 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:I.167, C:L.219 Water bridges: C:K.157 Salt bridges: C:R.156 Hydrogen bonds: J:L.22 PGV.15: 13 residues within 4Å: Chain C: L.31, W.34, M.40, L.43, L.47, T.51, M.54 Chain G: W.74, L.81 Ligands: PGV.13, PGV.17, PGV.19, PEK.24 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:L.81, G:L.81, C:L.31, C:W.34, C:W.34, C:L.43 PGV.16: 22 residues within 4Å: Chain A: D.227 Chain C: V.91, F.94, T.95, F.98, W.99, Y.102, H.103, L.106, A.107, P.108, T.109, V.248, F.251 Chain N: V.33, L.36, N.40, D.42, V.43, W.45 Ligands: PGV.3, CDL.18 20 PLIP interactions: 4 interactions with chain N, 16 interactions with chain C Hydrophobic interactions: N:L.36, N:V.43, N:W.45, N:W.45, C:V.91, C:F.94, C:T.95, C:F.98, C:W.99, C:W.99, C:Y.102, C:Y.102, C:Y.102, C:V.248, C:F.251, C:F.251 Hydrogen bonds: C:H.103, C:T.109 Salt bridges: C:H.103, C:H.103 PGV.17: 13 residues within 4Å: Chain C: V.171, T.174, L.175, A.178, S.179, Y.182, I.209, S.212, T.213, A.216 Ligands: PGV.15, PGV.22, PEK.24 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.171, C:T.174, C:A.178, C:I.209, C:I.209, C:A.216 Water bridges: C:Y.182 PGV.19: 26 residues within 4Å: Chain C: M.54, W.58, I.61, I.62, S.65, T.66, H.71, L.79, M.83, F.86, E.90, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Chain F: E.48 Ligands: PGV.13, PGV.15 27 PLIP interactions: 23 interactions with chain C, 4 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:I.62, C:F.86, C:F.86, C:I.210, C:I.210, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:S.65, C:H.231, F:Q.43, F:Q.43, F:E.48, F:E.48 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.22: 14 residues within 4Å: Chain C: V.129, Y.172, L.175, L.176, S.179 Chain G: T.44, S.47, W.48, S.51, G.52, H.53 Ligands: PGV.14, PGV.17, PEK.23 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:T.44, G:W.48, G:W.48, C:V.129, C:Y.172, C:L.175 Hydrogen bonds: G:W.48, G:S.51, G:G.52 Water bridges: G:L.49 Salt bridges: G:H.53 PGV.26: 13 residues within 4Å: Chain C: L.41, L.45 Chain J: M.57, T.58, L.59, L.61, G.62, G.63, V.65, Y.66, Y.69, W.73 Ligands: PGV.1 11 PLIP interactions: 8 interactions with chain J, 3 interactions with chain C Hydrophobic interactions: J:M.57, J:L.59, J:V.65, J:Y.66, J:Y.66, C:L.41, C:L.45, C:L.45 Hydrogen bonds: J:Y.66, J:Y.69 Water bridges: J:Y.69 PGV.27: 10 residues within 4Å: Chain A: V.419, M.423, I.453 Chain B: F.5 Chain D: I.111 Chain K: W.53, W.64, L.66, R.71 Ligands: CDL.10 9 PLIP interactions: 1 interactions with chain B, 5 interactions with chain K, 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:F.5, K:W.53, K:W.53, K:W.64, K:L.66, A:V.419, A:I.453, D:I.111 Salt bridges: K:R.71 PGV.28: 18 residues within 4Å: Chain A: F.2, L.18, L.21, F.22, W.25, F.102, F.109, L.110, L.113 Chain L: P.28, F.29, S.30, R.36, M.40, M.41, Y.44, F.45 Ligands: PGV.1 22 PLIP interactions: 8 interactions with chain L, 14 interactions with chain A Hydrophobic interactions: L:F.29, L:Y.44, L:Y.44, L:F.45, L:F.45, L:F.45, A:F.2, A:L.21, A:L.21, A:L.21, A:F.22, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.25, A:F.102, A:F.109, A:L.113 Hydrogen bonds: L:S.30 Salt bridges: L:R.36 PGV.29: 17 residues within 4Å: Chain A: N.406, Q.407, A.408, W.409, I.412 Chain D: T.106, F.109, F.113 Chain K: D.32, F.33, H.34, F.48 Chain M: P.36, Q.39, A.40, L.43, F.47 20 PLIP interactions: 5 interactions with chain M, 4 interactions with chain D, 6 interactions with chain K, 5 interactions with chain A Hydrophobic interactions: M:P.36, M:Q.39, M:L.43, M:F.47, D:T.106, D:F.109, D:F.109, D:F.113, K:F.33, K:F.33, K:F.48, A:A.408, A:W.409, A:W.409, A:I.412 Hydrogen bonds: M:Q.39, K:D.32, K:F.33, A:Q.407 Salt bridges: K:H.34

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

HEA.4: 33 residues within 4Å: Chain A: S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468, I.472 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:R.38, A:V.58, A:A.62, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:F.377, A:L.381, A:V.386, A:V.386, A:I.389, A:T.424, A:F.425, A:F.425, A:V.465, A:I.472 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.378, A:F.425 Metal complexes: A:H.378 HEA.5: 32 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, L.73 37 PLIP interactions: 33 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.126, A:W.236, A:V.243, A:V.243, A:V.243, A:Y.244, A:I.247, A:I.247, A:T.316, A:V.320, A:V.320, A:F.348, A:T.349, A:L.353, A:I.356, A:I.356, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:H.291 Water bridges: A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240, A:H.240 Metal complexes: A:H.376

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

CU.6: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.368, A:D.369, B:E.198

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 7 residues within 4Å: Chain A: E.40, L.41, Q.43, G.45, S.441, D.442, Y.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.43, A:G.45, A:D.442

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 21 residues within 4Å: Chain A: F.346, V.350, N.422, M.423, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, L.28, F.32, S.36, L.39 Chain I: V.33, F.36, Y.37, A.40, V.41, R.45 Ligands: PGV.27 21 PLIP interactions: 9 interactions with chain A, 3 interactions with chain I, 9 interactions with chain B Hydrophobic interactions: A:F.346, A:V.350, A:N.422, A:F.426, A:H.429, A:F.430, A:F.430, A:L.433, A:W.450, I:V.33, I:F.36, I:Y.37, B:L.7, B:L.7, B:L.7, B:L.28, B:L.28, B:F.32, B:F.32, B:F.32, B:L.39 CDL.18: 17 residues within 4Å: Chain A: I.165, I.169, V.193 Chain C: R.80, Y.81, I.84, I.87, I.88, V.91, W.240, H.243, F.244, V.247 Chain N: M.1 Ligands: PGV.2, PGV.3, PGV.16 16 PLIP interactions: 13 interactions with chain C, 1 interactions with chain N, 2 interactions with chain A Hydrophobic interactions: C:I.84, C:I.84, C:I.87, C:I.88, C:I.88, C:V.91, C:W.240, C:W.240, C:H.243, C:F.244, N:M.1, A:I.165, A:V.193 Hydrogen bonds: C:Y.81, C:Y.81 Salt bridges: C:R.80 CDL.20: 17 residues within 4Å: Chain A: W.334, L.339, K.411, V.415, F.418 Chain B: K.49 Chain D: M.93, N.94, R.95, S.96, T.97, N.98, W.100, K.101, I.103, V.104 Ligands: PGV.9 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:W.334, A:L.339, D:N.94, D:W.100, D:W.100

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.11: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.196, B:E.198, B:C.200, B:C.200, B:H.204

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.12: 23 residues within 4Å: Chain A: F.268, F.321, A.325, H.328 Chain B: L.37, I.41, M.45, H.52, M.56, D.57, A.58, E.60, V.61, I.64, W.65, L.68, P.69, I.72 Chain E: H.48 Chain I: A.16, L.19, R.20, I.23 20 PLIP interactions: 13 interactions with chain B, 6 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.37, B:I.41, B:A.58, B:E.60, B:V.61, B:I.64, B:W.65, B:W.65, B:P.69, B:I.72, A:F.268, A:F.321, A:F.321, A:A.325, A:H.328, I:R.20 Water bridges: B:D.57, B:D.57 Salt bridges: B:H.52, A:H.328

1 x ZN: ZINC ION(Non-covalent)

ZN.21: 4 residues within 4Å: Chain F: C.91, C.93, C.113, C.116 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.91, F:C.93, F:C.113, F:C.116

2 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.23: 15 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, A.168, L.169, Y.172 Chain F: A.32 Chain G: R.29, F.33, G.34, L.37, P.38 Ligands: PGV.14, PGV.22 15 PLIP interactions: 6 interactions with chain C, 1 interactions with chain F, 8 interactions with chain G Hydrophobic interactions: C:I.165, C:L.169, C:Y.172, C:Y.172, G:F.33, G:F.33, G:F.33, G:L.37, G:P.38 Hydrogen bonds: C:K.157, F:A.32 Salt bridges: C:K.157, G:R.29, G:R.29, G:R.29 PEK.24: 30 residues within 4Å: Chain A: H.151, A.203, T.207, L.210, L.215 Chain C: L.31, W.34, F.35, F.93, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, V.199, G.202, F.203, G.205, L.206 Chain G: W.74, T.80, L.81, F.82, H.83, N.88 Ligands: PGV.13, PGV.15, PGV.17 24 PLIP interactions: 7 interactions with chain G, 12 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: G:W.74, G:L.81, C:L.31, C:L.31, C:W.34, C:W.34, C:F.35, C:F.93, C:Y.181, C:I.188, C:V.199, C:F.203, A:A.203, A:T.207, A:L.210, A:L.215, A:L.215 Hydrogen bonds: G:T.80, G:L.81, G:F.82, G:N.84, G:N.88, C:Y.181, C:I.188

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.25: 8 residues within 4Å: Chain C: G.113, G.114 Chain H: W.31, Q.32, L.35, R.39 Chain N: E.52, W.54 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain H Hydrogen bonds: C:G.114, H:W.31, H:W.31 Salt bridges: H:R.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, W. et al., High-resolution in situ structures of mammalian respiratory supercomplexes. Nature (2024)

Release Date

2024-06-19

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: J
Cytochrome c oxidase subunit 7B: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8: M
Cytochrome c oxidase subunit NDUFA4: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4A

B
4B

C
4C

D
4D

E
4E

F
4F

G
4G

H
4H

I
4I

J
4J

K
4K

L
4L

M
4M

N
4N

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

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8

Cytochrome c oxidase subunit NDUFA4

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