SMTL ID : 8uge.1

In-situ complex III, state II

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)

CDL.1: 13 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 12 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A, 1 interactions with chain V Hydrophobic interactions: C:I.19, A:L.478, A:L.478, V:W.24 Hydrogen bonds: C:N.3, A:L.478, A:R.479, A:R.479 Salt bridges: C:R.5, C:H.221, C:H.221, A:R.479 CDL.8: 11 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45 Ligands: 3PE.9, CDL.16 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: C:W.30, C:W.30, C:F.33, G:V.38, G:V.38, G:T.42 Hydrogen bonds: C:S.29, C:S.29, C:W.30 Salt bridges: G:R.41, G:R.41, G:R.41 CDL.16: 24 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, I.92, K.227, L.230, G.231, F.234, M.235, I.238 Chain D: Y.305, K.308, R.309, K.316 Chain G: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.8 16 PLIP interactions: 4 interactions with chain D, 9 interactions with chain C, 3 interactions with chain G Hydrogen bonds: D:Y.305, C:N.32 Salt bridges: D:K.308, D:R.309, D:K.316, C:K.227, C:K.227, G:R.41, G:R.41 Hydrophobic interactions: C:F.33, C:I.92, C:L.230, C:F.234, C:F.234, C:I.238, G:I.35 CDL.24: 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.23, CDL.27 12 PLIP interactions: 1 interactions with chain P, 8 interactions with chain M, 3 interactions with chain Q Hydrogen bonds: P:Q.73, M:S.28, M:S.28, M:S.29, M:S.29, M:Y.104 Hydrophobic interactions: M:F.33, M:F.234, M:F.234 Salt bridges: Q:R.41, Q:R.41, Q:R.41 CDL.25: 12 residues within 4Å: Chain K: F.370, W.477, L.478, R.479 Chain M: N.3, R.5, I.19, H.221 Chain T: T.18 Chain U: W.24 Ligands: 3PE.17, 3PE.18 11 PLIP interactions: 4 interactions with chain M, 1 interactions with chain T, 5 interactions with chain K, 1 interactions with chain U Hydrophobic interactions: M:I.19, T:T.18, K:L.478, K:L.478, U:W.24 Hydrogen bonds: M:N.3, K:L.478, K:R.479 Salt bridges: M:R.5, M:H.221, K:R.479 CDL.27: 23 residues within 4Å: Chain M: S.29, N.32, F.33, M.89, C.93, K.227, L.230, G.231, F.234 Chain N: Y.305, K.308, R.309, K.316 Chain P: R.72, Q.73 Chain Q: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.24 21 PLIP interactions: 7 interactions with chain M, 5 interactions with chain Q, 7 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: M:N.32, M:F.33, M:F.234, M:F.234, M:F.234, Q:F.31, Q:I.35, Q:V.38, N:Y.305, N:Y.305 Hydrogen bonds: M:N.32, Q:N.37, N:Y.305, N:Y.305, N:K.316, P:M.71, P:Q.73 Salt bridges: M:K.227, Q:R.41, N:K.308, N:R.309

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

3PE.2: 7 residues within 4Å: Chain A: S.473, F.476, L.478 Chain C: H.221, T.225 Ligands: CDL.1, PC1.14 7 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:L.478 Hydrogen bonds: A:S.473, A:F.476 Salt bridges: D:K.311, C:H.221, C:H.221, C:H.221 3PE.3: 6 residues within 4Å: Chain A: F.370, R.479 Chain C: I.4, M.11, I.14 Ligands: CDL.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:R.479, C:I.4, C:I.14 Salt bridges: A:R.479 3PE.9: 15 residues within 4Å: Chain C: W.30, F.95, G.99, R.100, Y.103, Y.104, M.316, Q.322, F.325, W.326, V.329, L.332 Chain G: C.45, V.49 Ligands: CDL.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:Y.103, C:Y.104, C:F.325, C:W.326, C:W.326, C:V.329, C:V.329, C:L.332 Hydrogen bonds: C:Y.104, C:M.316, C:Q.322 3PE.10: 11 residues within 4Å: Chain C: L.160, W.163 Chain O: K.130, V.133, S.134, V.137, S.138, S.141 Chain U: W.34, A.35 Ligands: PC1.31 8 PLIP interactions: 2 interactions with chain U, 3 interactions with chain O, 3 interactions with chain C Hydrophobic interactions: U:W.34, U:A.35, O:K.130, O:V.137, C:L.160, C:W.163, C:W.163 Hydrogen bonds: O:S.141 3PE.12: 16 residues within 4Å: Chain C: L.43, L.82, M.236, L.240 Chain D: H.285, M.289, K.292, M.293, M.296 Chain E: Y.127, A.128, N.131, A.132, Q.135 Chain J: D.37 Ligands: PC1.14 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: C:L.43, C:L.82, C:L.240, C:L.240, D:M.293, E:A.132, E:Q.135 Salt bridges: D:H.285, D:K.292 Hydrogen bonds: E:N.131 3PE.15: 8 residues within 4Å: Chain D: P.302, A.306 Chain E: F.113, I.117 Chain G: R.25, A.26, F.27, Y.30 9 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 5 interactions with chain G Hydrophobic interactions: E:F.113, E:I.117, D:P.302, D:A.306, G:F.27, G:F.27, G:Y.30 Hydrogen bonds: G:A.26, G:F.27 3PE.17: 7 residues within 4Å: Chain K: F.370, R.479 Chain M: T.2, I.4, R.5, M.11 Ligands: CDL.25 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain K Hydrophobic interactions: M:R.5, K:R.479 Salt bridges: K:R.479, K:R.479 3PE.18: 8 residues within 4Å: Chain K: S.473, G.474, F.476, L.478 Chain M: H.221, I.229 Ligands: CDL.25, PC1.30 6 PLIP interactions: 2 interactions with chain K, 4 interactions with chain M Hydrogen bonds: K:S.473, K:F.476 Hydrophobic interactions: M:I.229 Salt bridges: M:H.221, M:H.221, M:H.221 3PE.23: 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, V.329 Chain Q: C.45, R.48 Ligands: CDL.24 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain Q Hydrophobic interactions: M:W.30, M:Y.103, M:Y.103, M:Y.104, M:F.325, M:F.325, M:V.329 Hydrogen bonds: M:Q.322, Q:R.48 3PE.28: 22 residues within 4Å: Chain M: L.43, L.46, L.82, M.236, L.240 Chain N: H.285, R.288, M.289, K.292, M.293, M.296, M.297 Chain O: Y.127, A.128, A.129, N.131, A.132, V.133, F.136, V.137 Chain T: D.37 Ligands: PC1.30 17 PLIP interactions: 4 interactions with chain N, 3 interactions with chain M, 10 interactions with chain O Hydrophobic interactions: N:M.293, N:M.296, M:L.43, M:L.82, M:L.240, O:A.128, O:A.129, O:A.132, O:V.133, O:V.133, O:F.136, O:F.136, O:V.137 Salt bridges: N:H.285, N:K.292 Hydrogen bonds: O:N.131, O:N.131 3PE.32: 8 residues within 4Å: Chain M: Y.155, I.156, D.159 Chain V: T.36, D.37, W.38, R.39, L.40 7 PLIP interactions: 4 interactions with chain V, 3 interactions with chain M Hydrophobic interactions: V:W.38, V:W.38, M:I.156 Hydrogen bonds: V:R.39, V:L.40, M:Y.155, M:D.159

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

HEM.4: 21 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, A.87, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:Q.44, C:L.51, C:L.51, C:Y.55, C:A.87, C:L.133, C:L.133, C:F.179, C:F.183 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.5: 23 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, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: U10.6 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.98, C:W.113, C:W.113, C:V.117, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206, 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 HEM.19: 19 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, Y.55, 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 11 PLIP interactions: 11 interactions with chain M, Hydrophobic interactions: M:Q.44, M:L.49, M:L.51, M:Y.55, M:L.133, M:F.179, M:F.183 Salt bridges: M:R.80, M:R.80 Metal complexes: M:H.83, M:H.182 HEM.20: 21 residues within 4Å: Chain M: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, I.189, H.196, L.197, L.200, S.205, N.206 Ligands: U10.21 19 PLIP interactions: 19 interactions with chain M, Hydrophobic interactions: M:L.37, M:V.98, M:W.113, M:W.113, M:V.117, M:L.119, M:L.120, M:I.189, M:L.197, 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 pi-Stacking: M:H.97 pi-Cation interactions: M:R.100 Metal complexes: M:H.97

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

U10.6: 13 residues within 4Å: Chain C: F.18, L.21, A.23, W.31, S.35, G.38, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEM.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.18, C:F.220 Hydrogen bonds: C:S.205 U10.7: 8 residues within 4Å: Chain C: M.124, F.128, I.146, P.270, F.274, A.277, Y.278, L.294 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.277, C:L.294 U10.21: 12 residues within 4Å: Chain M: A.17, F.18, L.21, W.31, S.35, G.38, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.20 No protein-ligand interaction detected (PLIP) U10.22: 8 residues within 4Å: Chain M: F.121, M.124, A.125, F.128, I.146, F.274, A.277, I.298 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:F.121, M:A.125, M:I.298

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

HEC.11: 19 residues within 4Å: Chain D: V.121, C.122, C.125, H.126, N.190, A.193, P.196, L.198, I.201, R.205, Y.211, V.212, L.215, L.216, F.238, A.244, M.245, P.248, I.249 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:V.121, D:N.190, D:A.193, 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 Hydrogen bonds: D:Y.211, D:Y.211 Salt bridges: D:R.205 Metal complexes: D:H.126 HEC.26: 24 residues within 4Å: Chain E: C.222 Chain N: V.117, V.121, C.122, C.125, H.126, N.190, A.193, P.195, P.196, 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, L.275 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:V.117, N:N.190, N:A.193, N:P.195, N:I.201, N:V.212, N:L.215, N:L.216, N:L.216, N:I.243, N:I.249, N:L.275 Hydrogen bonds: N:A.244 Salt bridges: N:R.205 Metal complexes: N:H.126

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

FES.13: 9 residues within 4Å: Chain E: C.217, T.218, H.219, C.222, C.236, H.239, S.241, Y.243, A.254 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.217, E:H.219, E:C.236, E:H.239 FES.29: 10 residues within 4Å: Chain O: C.217, H.219, L.220, G.221, C.222, C.236, C.238, H.239, G.240, S.241 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.217, O:H.219, O:C.236, 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 Chain C: I.39, I.229, L.233, M.236 Chain D: M.307 Chain E: Y.115, T.118, T.122, V.125 Chain J: F.15, R.16, T.18, F.21, A.22, I.25, A.26 Chain V: W.34 Ligands: 3PE.2, 3PE.12 15 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E, 1 interactions with chain V, 4 interactions with chain C, 5 interactions with chain J Salt bridges: A:D.451 pi-Cation interactions: A:F.476, E:Y.115, J:F.21 Hydrophobic interactions: E:V.125, E:V.125, V:W.34, C:I.39, C:I.229, C:I.229, C:L.233, J:A.22, J:I.25, J:I.25, J:A.26 PC1.30: 18 residues within 4Å: Chain K: D.451, F.476 Chain M: I.229, L.233, M.236 Chain N: M.307 Chain O: Y.115, T.118, T.122, V.125 Chain T: F.15, R.16, R.17, T.18, F.21, I.25 Ligands: 3PE.18, 3PE.28 10 PLIP interactions: 5 interactions with chain O, 2 interactions with chain T, 2 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: O:V.125, O:V.125, T:I.25, M:L.233 Hydrogen bonds: O:Y.115, O:T.118 pi-Cation interactions: O:Y.115, T:F.21, K:F.476 Salt bridges: K:D.451 PC1.31: 10 residues within 4Å: Chain C: Y.155, I.156, D.159 Chain U: L.32, T.36, D.37, W.38, R.39, L.40 Ligands: 3PE.10 8 PLIP interactions: 5 interactions with chain U, 3 interactions with chain C Hydrophobic interactions: U:L.32, U:T.36, U:W.38, C:Y.155 Hydrogen bonds: U:R.39, U:L.40 Salt bridges: C:D.159 pi-Cation interactions: C:Y.155

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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