SMTL ID : 9hzl.1

High resolution cryo-EM structure of human complex III in mitochondria

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-4-2-2-2-2-2-2-2-2-mer

Ligands

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 17 residues within 4Å: Chain A: V.38, R.41, I.42, S.45, F.46, V.49, V.50 Chain F: H.73 Chain I: S.28, A.29, W.30, F.33, I.92, L.96, Y.104 Ligands: CDL.8, PEE.11 12 PLIP interactions: 3 interactions with chain I, 8 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: I:W.30, I:W.30, A:V.38, A:F.46, A:F.46 Hydrogen bonds: I:A.29, A:S.45 Salt bridges: A:R.41, A:R.41, A:R.41, A:R.41, F:H.73 CDL.6: 17 residues within 4Å: Chain C: T.134, V.137, S.138, S.141 Chain G: L.32, A.35, T.36, D.37, W.38, R.39, L.40 Chain T: Y.155, I.156, D.159, L.160, W.163 Ligands: U10.14 7 PLIP interactions: 4 interactions with chain T, 3 interactions with chain G Hydrophobic interactions: T:I.156, T:W.163, T:W.163, T:W.163, G:W.38, G:W.38 Hydrogen bonds: G:R.39 CDL.8: 27 residues within 4Å: Chain A: V.30, G.34, I.35, N.37, V.38, R.41, I.42 Chain F: H.73 Chain H: V.300, Y.304, K.307, R.308, K.315 Chain I: A.29, N.32, F.33, L.36, M.89, C.93, K.227, L.230, G.231, L.234, F.235, L.237, S.238 Ligands: CDL.1 11 PLIP interactions: 3 interactions with chain H, 6 interactions with chain I, 2 interactions with chain A Hydrogen bonds: H:Y.304, H:R.308, A:R.41 Salt bridges: H:K.307, I:K.227, I:K.227 Hydrophobic interactions: I:A.29, I:F.33, I:L.234, I:F.235, A:I.35 CDL.12: 29 residues within 4Å: Chain A: R.3 Chain I: L.10, L.13, I.14, H.16, S.17, F.18, A.191, L.192, T.194, L.195, L.197, L.198, H.201 Chain L: R.3 Chain T: L.10, L.13, H.16, S.17, F.18, A.191, T.194, L.195, L.197, L.198, H.201 Ligands: U10.13, U10.14, U10.27 15 PLIP interactions: 5 interactions with chain T, 10 interactions with chain I Hydrophobic interactions: T:F.18, T:T.194, T:L.195, I:L.10, I:I.14, I:F.18, I:F.18, I:L.192, I:L.195, I:L.197 Salt bridges: T:H.16, T:H.201, I:H.16, I:H.201 Hydrogen bonds: I:H.16 CDL.15: 15 residues within 4Å: Chain G: W.24 Chain I: M.1, P.3, M.4, R.5, M.11, I.14, I.19, H.221 Chain K: F.370, R.470, L.478, R.479 Ligands: PLX.5, 3PE.16 9 PLIP interactions: 4 interactions with chain I, 1 interactions with chain G, 4 interactions with chain K Hydrophobic interactions: I:I.19, G:W.24, K:L.478 Hydrogen bonds: I:M.4, I:R.5, I:R.5, K:L.478 Salt bridges: K:R.479, K:R.479 CDL.19: 17 residues within 4Å: Chain I: Y.155, I.156, D.159, L.160, W.163 Chain N: V.133, T.134, V.137, S.138, S.141 Chain R: L.32, A.35, T.36, D.37, W.38, R.39 Ligands: U10.27 11 PLIP interactions: 5 interactions with chain R, 3 interactions with chain I, 3 interactions with chain N Hydrophobic interactions: R:L.32, R:T.36, R:W.38, R:W.38, I:L.160, I:W.163, N:V.137, N:V.137 Hydrogen bonds: R:R.39, I:D.159, N:S.138 CDL.23: 25 residues within 4Å: Chain L: Y.27, V.30, G.34, I.35, V.38, R.41 Chain Q: H.73 Chain S: V.300, P.301, Y.304, K.307, R.308, K.315 Chain T: A.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, F.235, S.238 Ligands: CDL.29 10 PLIP interactions: 6 interactions with chain S, 2 interactions with chain T, 2 interactions with chain L Hydrophobic interactions: S:V.300, T:L.234, L:V.38 Hydrogen bonds: S:Y.304, S:Y.304, T:N.32, L:R.41 Salt bridges: S:K.307, S:R.308, S:R.308 CDL.29: 15 residues within 4Å: Chain L: V.38, R.41, I.42, S.45, F.46, V.49, V.50 Chain Q: H.73 Chain S: Y.304 Chain T: S.28, A.29, W.30, F.33 Ligands: CDL.23, 3PE.28 14 PLIP interactions: 7 interactions with chain T, 6 interactions with chain L, 1 interactions with chain Q Hydrophobic interactions: T:W.30, T:W.30, T:W.30, T:F.33, T:F.33, L:V.38, L:I.42, L:F.46 Hydrogen bonds: T:A.29, T:W.30 Salt bridges: L:R.41, L:R.41, L:R.41, Q:H.73 CDL.30: 13 residues within 4Å: Chain R: W.24 Chain T: T.2, P.3, M.4, R.5, M.11 Chain V: F.370, W.477, L.478, R.479 Ligands: PC1.18, PLX.20, 3PE.31 10 PLIP interactions: 2 interactions with chain T, 6 interactions with chain V, 2 interactions with chain R Hydrophobic interactions: T:M.4, V:L.478, V:R.479, R:W.24, R:W.24 Hydrogen bonds: T:M.4, V:L.478, V:R.479 Salt bridges: V:R.479, V:R.479

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.2: 13 residues within 4Å: Chain A: R.25, A.26, Y.27 Chain C: R.93, L.94, E.95, R.110, F.113, S.114, V.117 Chain H: P.301, L.302, T.305 7 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: A:Y.27, C:R.110, H:L.302, H:T.305 Hydrogen bonds: A:Y.27 Salt bridges: A:R.25, C:R.93 3PE.4: 21 residues within 4Å: Chain C: Y.127, A.128, A.129, N.131, A.132, Q.135, F.136 Chain D: D.37 Chain H: H.284, R.287, M.288, K.291, M.292, M.295, M.296 Chain I: L.43, I.78, L.82, L.236, M.240 Ligands: PLX.5 6 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: H:M.292, I:L.43, I:I.78, C:A.128 Salt bridges: H:H.284, H:K.291 3PE.16: 10 residues within 4Å: Chain I: H.221, T.225, I.226, A.229 Chain K: S.473, G.474, F.476, L.478 Ligands: PLX.5, CDL.15 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:F.476 Salt bridges: I:H.221 3PE.21: 28 residues within 4Å: Chain N: V.125, Y.127, A.128, A.129, N.131, A.132, V.133, Q.135, F.136, V.137 Chain O: D.37 Chain S: H.284, R.287, M.288, K.291, M.292, M.295, M.296 Chain T: L.43, T.46, F.50, I.78, L.82, L.232, L.236, M.240 Ligands: PC1.18, U10.27 13 PLIP interactions: 3 interactions with chain T, 7 interactions with chain N, 2 interactions with chain S, 1 interactions with chain O Hydrophobic interactions: T:L.43, T:I.78, T:L.82, N:A.128, N:A.132, N:Q.135, N:F.136, N:F.136, N:F.136, N:V.137 Hydrogen bonds: S:H.284, O:D.37 Salt bridges: S:K.291 3PE.28: 14 residues within 4Å: Chain L: E.44, S.45, V.49 Chain T: W.30, L.96, G.99, R.100, Y.103, Y.104, M.316, Q.322, Y.325, W.326 Ligands: CDL.29 8 PLIP interactions: 8 interactions with chain T Hydrophobic interactions: T:W.30, T:W.30, T:Y.103, T:Y.103, T:Y.325 Hydrogen bonds: T:W.30, T:Y.103, T:Y.104 3PE.31: 10 residues within 4Å: Chain T: H.221, T.225, I.226, A.229 Chain V: S.473, G.474, F.476, L.478 Ligands: PC1.18, CDL.30 2 PLIP interactions: 2 interactions with chain T Hydrophobic interactions: T:A.229 Salt bridges: T:H.221

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

FES.3: 11 residues within 4Å: Chain C: C.217, H.219, L.220, C.222, C.236, C.238, H.239, S.241, Y.243, P.253, A.254 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.217, C:H.219, C:H.239 FES.17: 8 residues within 4Å: Chain N: H.219, L.220, C.236, C.238, H.239, S.241, L.251, G.252 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:H.219, N:H.219, N:H.239, N:S.241

2 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.5: 38 residues within 4Å: Chain C: Y.115, T.118, T.121, T.122, V.125, A.126, A.129, V.133 Chain D: Y.11, F.15, R.16, R.17, T.18, F.21, A.22, I.25, I.26 Chain G: W.24, G.28, G.31, L.32, W.34, A.35 Chain H: V.303, I.306, K.310 Chain I: I.226, A.229, L.232, L.233, L.236 Chain K: Y.450, D.451, F.476, L.478 Ligands: 3PE.4, CDL.15, 3PE.16 11 PLIP interactions: 3 interactions with chain K, 4 interactions with chain C, 1 interactions with chain I, 2 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: K:L.478, C:T.118, C:V.125, I:A.229, D:I.26, H:I.306 Salt bridges: K:D.451 pi-Cation interactions: K:F.476, C:Y.115, D:F.21 Hydrogen bonds: C:T.118 PLX.20: 19 residues within 4Å: Chain R: V.2, R.4, F.5, R.9, Y.10, L.13, V.14, W.17, V.18, T.20, A.21, W.24, G.25 Chain V: R.378, S.382, W.477, R.479 Ligands: U10.13, CDL.30 3 PLIP interactions: 3 interactions with chain R Hydrophobic interactions: R:W.17, R:W.17, R:W.24

2 x HEC: HEME C(Covalent)

HEC.7: 26 residues within 4Å: Chain H: V.116, V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, A.243, M.244, A.245, P.247, I.248, V.270, L.274 14 PLIP interactions: 14 interactions with chain H, Hydrophobic interactions: H:V.120, H:A.192, H:P.194, H:I.200, H:L.214, H:L.215, H:I.242, H:A.243, H:M.244 Hydrogen bonds: H:Y.210, H:Y.210, H:A.243 Salt bridges: H:R.204 Metal complexes: H:H.125 HEC.22: 26 residues within 4Å: Chain S: V.116, V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, A.243, M.244, P.247, I.248, V.270, L.274 11 PLIP interactions: 11 interactions with chain S, Hydrophobic interactions: S:V.120, S:A.192, S:P.194, S:L.197, S:I.200, S:L.215, S:P.247 Hydrogen bonds: S:A.243, S:M.244 Salt bridges: S:R.204 Metal complexes: S:H.125

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.9: 27 residues within 4Å: Chain I: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.84, A.87, F.91, T.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 11 PLIP interactions: 11 interactions with chain I, Hydrophobic interactions: I:L.41, I:Q.44, I:L.51, I:A.87, I:L.133, I:F.183, I:F.183, I:P.186 Salt bridges: I:R.80, I:R.80 Metal complexes: I:H.182 HEM.10: 29 residues within 4Å: Chain I: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, I.98, R.100, G.101, S.106, F.107, Y.109, T.112, W.113, G.116, I.117, L.119, L.120, T.123, A.193, H.196, L.197, L.200, S.205, N.206, L.301 Ligands: U10.14 20 PLIP interactions: 20 interactions with chain I, Hydrophobic interactions: I:L.37, I:L.37, I:I.98, I:W.113, I:W.113, I:L.119, I:L.119, I:L.120, I:L.197, I:L.200, I:L.200 Hydrogen bonds: I:W.31, I:W.31, I:G.34, I:S.106, I:N.206 Salt bridges: I:H.97, I:R.100, I:R.100 Metal complexes: I:H.97 HEM.24: 27 residues within 4Å: Chain T: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.84, A.87, T.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, Y.273 11 PLIP interactions: 11 interactions with chain T, Hydrophobic interactions: T:L.41, T:L.51, T:A.52, T:A.84, T:A.87, T:T.126, T:L.133, T:F.183 Salt bridges: T:R.80, T:R.80 Metal complexes: T:H.83 HEM.25: 28 residues within 4Å: Chain T: W.31, G.34, S.35, L.37, G.38, L.41, F.90, L.94, H.97, I.98, R.100, G.101, S.106, Y.109, T.112, W.113, G.116, I.117, L.119, L.120, T.123, A.193, H.196, L.197, L.200, S.205, N.206 Ligands: U10.27 18 PLIP interactions: 18 interactions with chain T, Hydrophobic interactions: T:L.37, T:L.37, T:I.98, T:I.98, T:T.112, T:L.119, T:L.120, T:T.123, T:L.197, T:L.200 Hydrogen bonds: T:W.31, T:S.106, T:S.205, T:N.206 Salt bridges: T:R.100, T:R.100 pi-Cation interactions: T:R.100 Metal complexes: T:H.97

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.11: 19 residues within 4Å: Chain A: S.45, V.49 Chain I: W.30, F.95, L.96, I.98, G.99, R.100, L.102, Y.103, Y.104, M.316, Q.322, Y.325, W.326, A.329, L.332, L.333 Ligands: CDL.1 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:W.30, I:W.30, I:W.30, I:F.95, I:I.98, I:Y.103, I:Y.103, I:Y.104, I:W.326, I:L.332, I:L.333 Hydrogen bonds: I:W.30, I:Y.103, I:Y.104

4 x U10: UBIQUINONE-10(Non-covalent)

U10.13: 31 residues within 4Å: Chain I: E.111, N.114, I.115, I.118, L.121, A.122, M.124, A.125, F.128, M.129, I.146, L.185, I.188, L.192, L.195, P.270, E.271, F.274, A.277, Y.278, L.281, L.294, L.295, L.299, A.302, M.303, I.306 Chain T: L.10 Ligands: CDL.12, PLX.20, U10.27 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:N.114, I:I.115, I:I.118, I:F.128, I:I.188, I:L.192, I:L.294, I:L.294, I:I.306, I:I.306 pi-Stacking: I:F.274 U10.14: 42 residues within 4Å: Chain C: M.140 Chain I: S.17, F.18, L.21, T.23, W.31, G.34, S.35, G.38, A.39, L.41, I.42, I.45, T.46, L.49, F.50, M.53, F.187, A.190, A.193, T.194, L.197, H.201, F.220, D.228 Chain T: A.125, F.128, M.129, I.146, T.147, L.149, L.150, W.163, I.164, F.181, I.184, L.185, I.188 Ligands: CDL.6, HEM.10, CDL.12, U10.26 15 PLIP interactions: 9 interactions with chain I, 6 interactions with chain T Hydrophobic interactions: I:F.18, I:I.42, I:I.45, I:I.45, I:T.46, I:A.190, I:T.194, I:L.197, T:A.125, T:I.146, T:L.149, T:L.150, T:F.181, T:F.181 Hydrogen bonds: I:S.35 U10.26: 24 residues within 4Å: Chain I: L.10 Chain T: S.110, E.111, T.112, N.114, I.115, I.118, L.121, A.122, M.124, A.125, F.128, I.146, L.149, L.185, I.188, L.192, L.195, F.199, F.274, A.277, L.294, I.306 Ligands: U10.14 14 PLIP interactions: 14 interactions with chain T Hydrophobic interactions: T:E.111, T:E.111, T:N.114, T:I.115, T:I.115, T:I.118, T:L.121, T:L.121, T:A.122, T:M.124, T:A.125, T:F.128, T:F.199 pi-Stacking: T:F.274 U10.27: 45 residues within 4Å: Chain I: A.125, F.128, M.129, I.146, T.147, L.149, L.150, W.163, I.164, R.177, F.178, F.181, I.184, I.188 Chain N: M.140 Chain T: F.18, L.21, T.23, W.31, N.32, G.34, S.35, G.38, A.39, L.41, I.42, I.45, T.46, L.49, F.50, M.53, F.187, A.190, A.193, T.194, L.197, H.201, S.205, F.220, D.228 Ligands: CDL.12, U10.13, CDL.19, 3PE.21, HEM.25 17 PLIP interactions: 7 interactions with chain I, 10 interactions with chain T Hydrophobic interactions: I:F.128, I:L.150, I:W.163, I:I.164, I:F.181, I:F.181, I:F.181, T:F.18, T:I.42, T:I.45, T:I.45, T:T.46, T:L.49, T:F.50, T:A.193, T:L.197 Hydrogen bonds: T:D.228

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.18: 32 residues within 4Å: Chain N: Y.115, T.118, T.121, T.122, V.125, A.128 Chain O: F.15, R.16, T.18, F.21, A.22, I.25, I.26 Chain R: W.24, V.27, G.28 Chain S: M.296, L.299, V.303, I.306 Chain T: I.226, A.229, L.230, L.232, L.233, L.236 Chain V: D.451, F.476, L.478 Ligands: 3PE.21, CDL.30, 3PE.31 14 PLIP interactions: 3 interactions with chain O, 3 interactions with chain T, 5 interactions with chain N, 2 interactions with chain V, 1 interactions with chain S Hydrophobic interactions: O:F.21, O:A.22, T:A.229, T:L.232, T:L.233, N:T.118, N:T.121, V:L.478, S:L.299 pi-Cation interactions: O:F.21, N:Y.115, V:F.476 Hydrogen bonds: N:T.118, N:T.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, M.D. et al., Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome. To Be Published

Release Date

2025-11-12

Peptides

Cytochrome b-c1 complex subunit 8: AL
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BCMN
Cytochrome b-c1 complex subunit 9: DO
Cytochrome b-c1 complex subunit 6, mitochondrial: EP
Cytochrome b-c1 complex subunit 7: FQ
Cytochrome b-c1 complex subunit 10: GR
Cytochrome c1, heme protein, mitochondrial: HS
Cytochrome b: IT
Cytochrome b-c1 complex subunit 2, mitochondrial: JU
Cytochrome b-c1 complex subunit 1, mitochondrial: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
N

B
B

C
C

M
O

N
P

D
D

O
Q

E
E

P
R

F
F

Q
S

G
G

R
T

H
H

S
U

I
J

T
V

J
K

U
W

K
L

V
Y

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 10

Cytochrome c1, heme protein, mitochondrial

Cytochrome b

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b-c1 complex subunit 1, mitochondrial

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