SMTL ID : 8ugg.1

In-situ complex III, state IV

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, R.470, W.477, L.478, R.479 Chain C: R.5, F.18, H.221, T.225 Chain V: W.24 Ligands: 3PE.2, 3PE.3, PC1.14 12 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C, 1 interactions with chain V Hydrophobic interactions: A:L.478, A:L.478, C:F.18, C:T.225, V:W.24 Hydrogen bonds: A:L.478, A:R.479 Salt bridges: A:R.479, C:R.5, C:R.5, C:H.221, C:H.221 CDL.12: 23 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, K.227, G.231, F.234, M.235 Chain D: Y.305, K.308, R.309, K.316 Chain F: M.71, R.72 Chain G: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.16 18 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D, 4 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:N.32, C:F.33, C:L.36, C:K.227, C:F.234, C:F.234, C:F.234, G:I.35 Salt bridges: C:K.227, D:K.308, D:K.316, G:R.41, G:R.41 Hydrogen bonds: D:Y.305, D:R.309, D:K.316, G:N.37, F:M.71 CDL.16: 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.8, CDL.12 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:W.30, C:F.33, G:V.38 Hydrogen bonds: C:S.29, C:S.29, C:W.30 Salt bridges: G:R.41, G:R.41, G:R.41 CDL.18: 11 residues within 4Å: Chain K: F.370, R.470, W.477, L.478, R.479 Chain M: N.3, R.5, I.19, H.221 Ligands: 3PE.17, 3PE.19 8 PLIP interactions: 4 interactions with chain K, 4 interactions with chain M Hydrophobic interactions: K:L.478, M:I.19, M:I.19 Hydrogen bonds: K:L.478, K:R.479 Salt bridges: K:R.479, M:R.5, M:H.221 CDL.25: 13 residues within 4Å: Chain M: S.28, S.29, W.30, F.33, F.234 Chain P: Q.73 Chain Q: V.38, R.41, T.42, C.45, I.46 Ligands: 3PE.24, CDL.27 12 PLIP interactions: 7 interactions with chain M, 5 interactions with chain Q Hydrophobic interactions: M:W.30, M:F.33, M:F.234, M:F.234, Q:T.42 Hydrogen bonds: M:S.28, M:S.29, M:S.29, Q:R.41 Salt bridges: Q:R.41, Q:R.41, Q:R.41 CDL.27: 26 residues within 4Å: Chain M: S.29, N.32, F.33, L.36, C.93, K.227, L.230, G.231, F.234, M.235 Chain N: L.301, Y.305, K.308, R.309, K.316 Chain P: M.71, R.72, Q.73 Chain Q: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.25 22 PLIP interactions: 5 interactions with chain M, 10 interactions with chain N, 5 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: M:F.33, M:F.234, M:F.234, M:F.234, M:M.235, N:L.301, N:Y.305, N:Y.305, N:Y.305, Q:F.31, Q:I.35, Q:V.38 Hydrogen bonds: N:Y.305, N:K.316, Q:N.37, P:R.72, P:Q.73 Salt bridges: N:K.308, N:R.309, N:R.309, N:K.316, Q:R.41

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

3PE.2: 8 residues within 4Å: Chain A: S.473, G.474, F.476, L.478 Chain C: H.221, T.225 Ligands: CDL.1, PC1.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Salt bridges: C:H.221, C:H.221, C:H.221 Hydrogen bonds: A:S.473 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 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:R.479, C:I.4, C:R.5, C:I.14 Salt bridges: A:R.479 Hydrogen bonds: C:T.2, C:N.3, C:I.4 3PE.8: 15 residues within 4Å: Chain C: W.30, F.95, I.96, G.99, R.100, Y.103, Y.104, M.316, Q.322, F.325, W.326, L.332 Chain G: C.45, R.48 Ligands: CDL.16 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:I.96, C:I.96, C:R.100, C:Y.103, C:Y.103, C:Y.103, C:F.325, C:W.326, C:W.326, C:L.332 Hydrogen bonds: C:M.316, C:Q.322, G:R.48 3PE.9: 12 residues within 4Å: Chain C: D.159, W.163 Chain M: N.74 Chain O: K.130, V.133, S.134, V.137, S.138, S.141 Chain U: W.34, A.35 Ligands: PC1.31 12 PLIP interactions: 6 interactions with chain O, 1 interactions with chain U, 1 interactions with chain M, 4 interactions with chain C Hydrophobic interactions: O:K.130, O:V.133, O:V.137, O:V.137, U:W.34, C:W.163, C:W.163, C:W.163, C:W.163 Hydrogen bonds: O:S.141, O:S.141, M:N.74 3PE.11: 13 residues within 4Å: Chain C: M.236, L.240 Chain D: H.285, R.288, M.289, K.292, M.293, M.296, M.297 Chain E: Y.127, A.128, N.131 Chain J: D.37 13 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: C:M.236, C:L.240, E:Y.127, E:A.128 Hydrogen bonds: C:Y.75, D:R.288, D:K.292, D:M.293, E:Y.127, E:Y.127, E:N.131 Salt bridges: D:H.285, D:K.292 3PE.15: 8 residues within 4Å: Chain D: P.302 Chain E: F.113, I.117 Chain G: R.25, A.26, F.27, Y.30, F.31 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.27, G:Y.30, G:F.31, G:F.31 Hydrogen bonds: G:R.25, G:A.26, G:F.27 3PE.17: 8 residues within 4Å: Chain K: R.479 Chain M: M.1, T.2, I.4, R.5, M.11 Chain U: W.24 Ligands: CDL.18 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain K Hydrogen bonds: M:M.1, M:T.2 Salt bridges: K:R.479, K:R.479 3PE.19: 8 residues within 4Å: Chain K: S.473, G.474, F.476, L.478 Chain M: H.221, I.229 Ligands: CDL.18, 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.24: 13 residues within 4Å: Chain M: W.30, F.95, G.99, R.100, Y.103, Y.104, M.316, Q.322, W.326 Chain Q: R.48, V.49, F.53 Ligands: CDL.25 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain Q Hydrophobic interactions: M:W.30, M:W.30, M:Y.103, M:Y.103, M:W.326, M:W.326, Q:F.53 Hydrogen bonds: M:Q.322, Q:R.48 3PE.29: 19 residues within 4Å: Chain M: Y.75, L.82, L.240 Chain N: H.285, R.288, M.289, K.292, M.293, M.296, M.297 Chain O: Y.127, A.128, N.131, A.132, V.133, Q.135, F.136 Chain T: D.37 Ligands: PC1.30 15 PLIP interactions: 9 interactions with chain O, 3 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: O:A.128, O:A.132, O:V.133, O:F.136, O:F.136, O:F.136, N:M.293, M:L.82, M:L.240 Hydrogen bonds: O:N.131, O:N.131, O:Q.135, M:Y.75 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 12 PLIP interactions: 6 interactions with chain V, 6 interactions with chain M Hydrophobic interactions: V:L.32, V:T.36, V:W.38, V:W.38, V:W.38, M:Y.155, M:I.156, M:L.160 Hydrogen bonds: V:R.39, M:Y.155, 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, R.80, H.83, A.84, A.87, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, I.189, Y.273 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:L.133, C:L.133, C:F.179, C:F.183, C:I.189 Salt bridges: C:R.80, C:R.80 Metal complexes: 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: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:S.106, 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: 23 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, A.87, V.123, T.126, A.127, G.130, L.133, P.134, F.179, H.182, F.183, P.186, I.189, Y.273 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:I.45, M:L.49, M:L.51, M:L.51, M:Y.55, M:V.123, M:T.126, M:A.127, M:L.133, M:L.133, M:F.179, M:F.183, M:I.189 Salt bridges: M:R.80, M:R.80 pi-Stacking: M:H.182 Metal complexes: M:H.83, M:H.182 HEM.21: 23 residues within 4Å: Chain M: 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: U10.22 19 PLIP interactions: 19 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:V.98, M:F.109, M:W.113, M:V.117, M:L.119, M:L.120, 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 pi-Cation interactions: M:R.100 Metal complexes: M:H.97

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

U10.6: 16 residues within 4Å: Chain C: F.18, L.21, A.23, W.31, S.35, G.38, T.190, A.193, A.194, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEM.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.18, C:T.190, C:A.193, C:L.197, C:F.220, C:F.220 Hydrogen bonds: C:S.205 U10.7: 11 residues within 4Å: Chain C: F.121, M.124, A.125, F.128, I.146, P.270, F.274, A.277, Y.278, L.294, I.298 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.121, C:M.124, C:A.125, C:A.277, C:L.294, C:I.298 U10.22: 15 residues within 4Å: Chain M: A.17, F.18, L.21, W.31, S.35, G.38, L.41, I.42, T.190, A.193, L.197, H.201, F.220, D.228 Ligands: HEM.21 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:F.18, M:L.41, M:I.42, M:I.42, M:T.190, M:A.193, M:L.197, M:L.197 pi-Stacking: M:F.220 U10.23: 11 residues within 4Å: Chain M: M.124, A.125, F.128, M.129, I.146, L.150, I.164, F.181, F.274, A.277, L.294 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:A.125, M:F.128, M:L.150, M:I.164, M:F.181, M:F.181

2 x HEC: HEME C(Non-covalent)

HEC.10: 19 residues within 4Å: Chain D: V.121, C.122, C.125, H.126, N.190, A.193, L.194, P.196, I.201, R.205, Y.211, L.216, F.238, A.244, M.245, P.248, I.249, V.271 Chain O: H.239 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:V.121, D:N.190, D:A.193, D:P.196, D:I.201, D:L.216, D:F.238, D:A.244, D:P.248, D:I.249, D:V.271 Hydrogen bonds: D:Y.211 Salt bridges: D:R.205 Metal complexes: D:H.126 HEC.26: 21 residues within 4Å: Chain N: 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.215, L.216, F.238, I.243, A.244, M.245, P.248, I.249, V.271 13 PLIP interactions: 13 interactions with chain N, Hydrophobic interactions: N:V.121, N:N.190, N:A.193, N:P.195, N:P.196, N:I.201, N:L.215, N:L.216, N:L.216, N:P.248, N:I.249 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, C.238, H.239, S.241, 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.28: 8 residues within 4Å: Chain O: C.217, H.219, L.220, G.221, C.236, C.238, H.239, S.241 5 PLIP interactions: 5 interactions with chain O, Metal complexes: O:C.217, O:H.219, O:C.236, O:C.238, O:H.239

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

PC1.14: 18 residues within 4Å: Chain A: D.451, F.476 Chain C: I.229, M.236 Chain E: Y.115, T.118, T.122, V.125 Chain J: F.15, R.16, T.18, F.21, A.22, I.25 Chain V: G.31, W.34 Ligands: CDL.1, 3PE.2 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain J, 1 interactions with chain V Hydrophobic interactions: E:V.125, C:I.229, J:I.25, V:W.34 pi-Cation interactions: E:Y.115 Salt bridges: A:D.451 PC1.30: 19 residues within 4Å: Chain K: D.451, F.476, L.478 Chain M: I.39, I.229, A.232, M.236 Chain N: M.307 Chain O: Y.115, T.118, T.122, V.125 Chain T: F.15, T.18, F.21, A.22, I.25 Ligands: 3PE.19, 3PE.29 12 PLIP interactions: 3 interactions with chain M, 3 interactions with chain K, 5 interactions with chain O, 1 interactions with chain T Hydrophobic interactions: M:I.39, M:I.229, M:A.232, K:L.478, O:V.125, O:V.125, T:I.25 Salt bridges: K:D.451 pi-Cation interactions: K:F.476, O:Y.115 Hydrogen bonds: O:Y.115, O:T.118 PC1.31: 9 residues within 4Å: Chain C: Y.155, I.156, D.159 Chain U: T.36, D.37, W.38, R.39, L.40 Ligands: 3PE.9 5 PLIP interactions: 4 interactions with chain U, 1 interactions with chain C Hydrophobic interactions: U:W.38, U:W.38, C:I.156 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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