SMTL ID : 8ugf.1

In-situ complex III, state III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.1: 14 residues within 4Å: Chain A: F.370, W.477, L.478, R.479 Chain C: N.3, R.5, F.18, I.19, H.221, T.225 Chain V: W.24 Ligands: 3PE.2, 3PE.3, PC1.14 14 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A, 1 interactions with chain V Hydrophobic interactions: C:F.18, C:I.19, C:T.225, A:L.478, A:L.478, V:W.24 Hydrogen bonds: C:N.3, A:L.478, A:R.479 Salt bridges: C:R.5, C:R.5, C:H.221, C:H.221, A:R.479 CDL.8: 10 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Chain F: Q.73 Chain G: R.41, T.42, C.45 Ligands: 3PE.9, CDL.16 8 PLIP interactions: 6 interactions with chain C, 1 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:F.33 Hydrogen bonds: C:S.29, C:S.29, C:W.30, F:Q.73 Salt bridges: G:R.41 CDL.16: 20 residues within 4Å: Chain C: S.29, N.32, L.36, K.227, L.230, G.231, F.234, M.235 Chain D: Y.305, K.308, R.309, K.316 Chain F: R.72 Chain G: Y.30, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.8 16 PLIP interactions: 1 interactions with chain F, 4 interactions with chain D, 7 interactions with chain C, 4 interactions with chain G Hydrogen bonds: F:R.72, D:Y.305, D:R.309, G:N.37 Salt bridges: D:K.308, D:K.316, C:K.227, G:R.41, G:R.41 Hydrophobic interactions: C:N.32, C:L.36, C:L.230, C:F.234, C:F.234, C:M.235, G:I.35 CDL.18: 11 residues within 4Å: Chain K: F.370, W.477, L.478, R.479 Chain M: N.3, R.5, I.19, H.221 Chain U: W.24 Ligands: 3PE.17, 3PE.19 11 PLIP interactions: 4 interactions with chain K, 5 interactions with chain M, 2 interactions with chain U Hydrophobic interactions: K:L.478, M:I.19, U:W.24, U:W.24 Hydrogen bonds: K:L.478, K:R.479, M:N.3, M:N.3 Salt bridges: K:R.479, M:R.5, M:H.221 CDL.29: 22 residues within 4Å: Chain M: S.29, N.32, F.33, L.36, K.227, L.230, G.231, F.234 Chain N: Y.305, K.308, R.309, K.316 Chain P: M.71, R.72, Q.73 Chain Q: Y.30, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.30 20 PLIP interactions: 7 interactions with chain M, 9 interactions with chain N, 3 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:N.32, M:F.33, M:L.36, M:F.234, M:F.234, N:Y.305, N:Y.305, Q:I.35, Q:V.38 Hydrogen bonds: M:N.32, N:Y.305, N:Y.305, N:K.316, P:M.71 Salt bridges: M:K.227, N:K.308, N:R.309, N:R.309, N:K.316, Q:R.41 CDL.30: 13 residues within 4Å: Chain M: S.28, S.29, W.30, F.33, Y.104, F.234 Chain P: Q.73 Chain Q: V.38, R.41, T.42, C.45 Ligands: 3PE.24, CDL.29 12 PLIP interactions: 7 interactions with chain M, 4 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:W.30, M:F.33, M:F.234, Q:T.42 Hydrogen bonds: M:S.28, M:S.29, M:S.29, M:W.30, P:Q.73 Salt bridges: Q:R.41, Q:R.41, Q:R.41

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

3PE.2: 7 residues within 4Å: Chain A: S.473, G.474, F.476, L.478 Chain C: H.221 Ligands: CDL.1, PC1.14 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: A:S.473, A:F.476 Salt bridges: D:K.311, C:H.221, C:H.221, C:H.221 3PE.3: 9 residues within 4Å: Chain A: F.370, R.479 Chain C: T.2, N.3, I.4, R.5, M.11, I.14 Ligands: CDL.1 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:R.5, C:I.14 Hydrogen bonds: C:N.3, C:I.4 Salt bridges: A:R.479 3PE.9: 18 residues within 4Å: Chain C: W.30, F.95, I.96, V.98, G.99, R.100, Y.103, Y.104, M.316, Q.322, F.325, W.326, V.329, L.332 Chain F: A.25 Chain G: C.45, V.49 Ligands: CDL.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:V.98, C:Y.103, C:F.325, C:V.329, C:L.332 Hydrogen bonds: C:Y.103, C:M.316, C:Q.322 3PE.10: 10 residues within 4Å: Chain C: D.159, W.163 Chain O: K.130, V.133, S.134, V.137, S.138, S.141 Chain U: A.35 Ligands: PC1.31 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain O Hydrophobic interactions: C:W.163, O:K.130, O:V.133 Hydrogen bonds: O:S.141, O:S.141 3PE.13: 13 residues within 4Å: Chain C: M.236, L.240 Chain D: H.285, M.289, K.292, M.293, M.296, M.297 Chain E: Y.127, A.128, N.131, A.132 Chain J: D.37 8 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: C:L.240, D:M.293, D:M.296, E:A.128, E:A.132 Salt bridges: D:H.285, D:K.292 Hydrogen bonds: E:N.131 3PE.15: 10 residues within 4Å: Chain D: P.302, A.306 Chain E: R.93, F.113, I.117 Chain G: R.25, A.26, F.27, Y.30, F.31 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:F.27, G:F.27, G:Y.30, G:F.31, D:A.306 Hydrogen bonds: G:A.26, G:F.27 3PE.17: 8 residues within 4Å: Chain K: F.370, R.479 Chain M: T.2, I.4, R.5, M.11 Chain U: W.24 Ligands: CDL.18 5 PLIP interactions: 2 interactions with chain K, 2 interactions with chain M, 1 interactions with chain U Salt bridges: K:R.479, K:R.479 Hydrophobic interactions: M:I.4, M:R.5, U:W.24 3PE.19: 7 residues within 4Å: Chain K: S.473, F.476, L.478 Chain M: H.221, I.229 Ligands: CDL.18, PC1.28 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain K Salt bridges: M:H.221, M:H.221 Hydrogen bonds: K:S.473 3PE.24: 14 residues within 4Å: Chain M: W.30, F.95, G.99, R.100, Y.103, Y.104, M.316, Q.322, F.325, W.326 Chain Q: C.45, R.48, F.53 Ligands: CDL.30 11 PLIP interactions: 9 interactions with chain M, 2 interactions with chain Q Hydrophobic interactions: M:W.30, M:W.30, M:F.95, M:Y.103, M:F.325, M:W.326, Q:F.53 Hydrogen bonds: M:Y.104, M:M.316, M:Q.322, Q:R.48 3PE.27: 19 residues within 4Å: Chain M: L.43, L.46, L.82, M.236 Chain N: H.285, M.289, K.292, M.293, M.297 Chain O: Y.127, A.128, A.129, N.131, A.132, V.133, Q.135, F.136 Chain T: D.37 Ligands: PC1.28 12 PLIP interactions: 6 interactions with chain O, 3 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: O:A.132, O:A.132, O:V.133, O:V.133, O:F.136, M:L.43, M:L.46, M:L.82, N:M.293 Hydrogen bonds: O:N.131 Salt bridges: N:H.285, N:K.292 3PE.32: 10 residues within 4Å: Chain M: Y.155, I.156, D.159, L.160 Chain V: L.32, T.36, D.37, W.38, R.39, L.40 11 PLIP interactions: 6 interactions with chain M, 5 interactions with chain V Hydrophobic interactions: M:Y.155, M:I.156, M:L.160, V:L.32, V:W.38, V:W.38 Hydrogen bonds: M:Y.155, M:Y.155, M:Y.155, V:R.39, V:L.40

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

HEM.4: 19 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, R.80, H.83, A.87, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:T.126, C:L.133, C:L.133, C:F.179, C:F.183, C:F.183 Hydrogen bonds: C:N.255 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.5: 22 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, H.196, L.197, L.200, S.205, N.206 Ligands: U10.6 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:W.113, C:V.117, C:L.119, C:L.197, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Stacking: C:H.97 pi-Cation interactions: C:R.100 Metal complexes: C:H.196 HEM.20: 19 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, A.52, R.80, H.83, A.87, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 10 PLIP interactions: 10 interactions with chain M, Hydrophobic interactions: M:Q.44, M:L.51, M:T.126, M:L.133, M:L.133, M:F.179, M:F.183 Salt bridges: M:R.80, M:R.80 Metal complexes: M:H.83 HEM.21: 21 residues within 4Å: Chain M: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, V.117, L.119, I.189, H.196, L.197, L.200, S.205, N.206 Ligands: U10.22 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:V.98, M:W.113, M:W.113, M:V.117, M:L.119, M:I.189, M:L.197, M:L.200, M:L.200 Hydrogen bonds: M:G.34, M:S.106, M:N.206 Salt bridges: M:H.97, M:R.100, M:R.100 Metal complexes: M:H.196

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

U10.6: 12 residues within 4Å: Chain C: A.17, L.21, A.23, S.35, G.38, L.41, A.194, L.200, H.201, F.220, D.228 Ligands: HEM.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.41, C:A.194, C:F.220 U10.7: 9 residues within 4Å: Chain C: M.124, A.125, F.128, I.146, P.270, F.274, A.277, L.294, I.298 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.125, C:A.277, C:L.294, C:I.298 U10.22: 13 residues within 4Å: Chain M: A.17, F.18, W.31, S.35, G.38, I.42, I.45, T.190, L.197, H.201, F.220, D.228 Ligands: HEM.21 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:F.18, M:I.42, M:I.42, M:I.45 U10.23: 13 residues within 4Å: Chain M: F.121, M.124, A.125, F.128, M.129, I.146, W.163, I.164, F.181, F.274, A.277, L.294, I.298 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:F.121, M:I.146, M:W.163, M:I.164, M:F.181, M:F.181

2 x HEC: HEME C(Non-covalent)(Covalent)

HEC.11: 23 residues within 4Å: Chain D: V.121, C.122, C.125, H.126, N.190, A.193, L.194, P.195, P.196, L.198, I.201, R.205, Y.211, V.212, L.215, L.216, F.238, I.243, A.244, M.245, P.248, I.249, V.271 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:V.121, D:P.195, D:P.196, D:L.198, D:I.201, D:V.212, D:L.215, D:L.216, D:A.244, D:P.248, D:I.249, D:V.271 Hydrogen bonds: D:Y.211, D:Y.211, D:A.244, D:M.245 Salt bridges: D:R.205 Metal complexes: D:H.126 HEC.25: 21 residues within 4Å: Chain N: V.117, V.121, C.122, C.125, H.126, N.190, A.193, L.194, P.195, P.196, I.201, R.205, Y.211, L.216, F.238, I.243, A.244, M.245, P.248, I.249, V.271 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.117, N:N.190, N:A.193, N:P.195, N:P.196, N:I.201, N:L.216, N:L.216, N:I.243, N:P.248, N:I.249, N:V.271 Hydrogen bonds: N:Y.211 Salt bridges: N:R.205 pi-Stacking: N:H.126 Metal complexes: N:H.126

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

FES.12: 9 residues within 4Å: Chain E: C.217, T.218, H.219, G.221, C.222, P.224, C.236, H.239, Y.243 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.217, E:H.219, E:C.236, E:C.236, E:H.239 FES.26: 10 residues within 4Å: Chain O: C.217, T.218, H.219, G.221, C.236, C.238, H.239, S.241, Y.243, A.254 5 PLIP interactions: 5 interactions with chain O, Metal complexes: O:C.217, O:H.219, O:C.236, O:H.239, O:H.239

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

PC1.14: 21 residues within 4Å: Chain A: D.451, F.476, L.478 Chain C: I.39, I.229, M.236 Chain D: M.307 Chain E: Y.115, T.118, T.121, T.122, V.125 Chain J: F.15, R.16, T.18, F.21, I.25 Chain V: G.31, W.34 Ligands: CDL.1, 3PE.2 10 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 3 interactions with chain E, 2 interactions with chain J, 1 interactions with chain V Hydrophobic interactions: C:I.39, C:I.229, A:L.478, E:T.121, E:V.125, J:I.25, J:I.25, V:W.34 Salt bridges: A:D.451 pi-Cation interactions: E:Y.115 PC1.28: 20 residues within 4Å: Chain K: D.451, F.476 Chain M: I.39, I.229, A.232, M.236 Chain N: M.307 Chain O: Y.115, T.118, T.121, T.122, V.125 Chain T: F.15, R.16, T.18, F.21, A.22, I.25 Ligands: 3PE.19, 3PE.27 13 PLIP interactions: 7 interactions with chain O, 2 interactions with chain K, 2 interactions with chain T, 2 interactions with chain M Hydrophobic interactions: O:T.121, O:T.122, O:V.125, O:V.125, T:A.22, T:I.25, M:I.39, M:A.232 Hydrogen bonds: O:Y.115, O:T.118 pi-Cation interactions: O:Y.115, K:F.476 Salt bridges: K:D.451 PC1.31: 9 residues within 4Å: Chain C: Y.155, I.156, D.159 Chain U: L.32, T.36, D.37, W.38, R.39 Ligands: 3PE.10 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain U Hydrophobic interactions: C:I.156, U:L.32, U:W.38, U:W.38 pi-Cation interactions: C:Y.155 Hydrogen bonds: U:R.39, U:L.40

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 b-c1 complex subunit 1, mitochondrial: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EIOS
Cytochrome b-c1 complex subunit 7: FP
Cytochrome b-c1 complex subunit 8: GQ
Cytochrome b-c1 complex subunit 6, mitochondrial: HR
Ubiquinol-cytochrome c reductase complex 7.2 kDa protein: JT
Cytochrome b-c1 complex subunit 10: UV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3A

K
3N

B
3B

L
3O

C
3C

M
3P

D
3D

N
3Q

E
3E

I
3I

O
3R

S
3V

F
3F

P
3S

G
3G

Q
3T

H
3H

R
3U

J
3J

T
3W

U
3X

V
3Y

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Ubiquinol-cytochrome c reductase complex 7.2 kDa protein

Cytochrome b-c1 complex subunit 10

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