SMTL ID : 8iar.1

Respiratory complex CIII2, focus-refined of type I, Wild type mouse under thermoneutral temperature

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine

3PE.1: 7 residues within 4Å: Chain A: S.473, F.476, L.478 Chain C: H.221, T.225, I.229 Chain D: K.310 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:I.229 Salt bridges: C:H.221, C:H.221, D:K.310 Hydrogen bonds: A:S.473, A:F.476 3PE.4: 15 residues within 4Å: Chain C: W.30, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, M.316, Y.325, W.326, L.332 Chain G: R.45 Ligands: CDL.8 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:L.96, C:V.98, C:L.102, C:Y.103, C:Y.103, C:Y.104, C:W.326, C:L.332 Hydrogen bonds: C:Y.104 Salt bridges: G:R.45 3PE.10: 21 residues within 4Å: Chain C: P.319, I.320, I.323, I.327, A.330, N.331, I.334, L.353, A.354, S.357 Chain F: W.20, Y.21, A.24 Chain G: R.43, E.44, L.47, R.48, P.51, P.52, V.55, I.59 18 PLIP interactions: 7 interactions with chain G, 2 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: G:L.47, G:P.51, G:P.52, G:P.52, G:V.55, G:I.59, F:W.20, F:A.24, C:I.323, C:I.323, C:I.327, C:I.327, C:A.330, C:N.331, C:I.334, C:L.353, C:A.354 Salt bridges: G:R.48 3PE.11: 9 residues within 4Å: Chain L: S.473, F.476, L.478 Chain N: H.221, T.225, I.229 Chain O: K.310 Ligands: CDL.12, PC1.19 7 PLIP interactions: 4 interactions with chain N, 2 interactions with chain L, 1 interactions with chain O Hydrophobic interactions: N:T.225, N:I.229 Salt bridges: N:H.221, N:H.221, O:K.310 Hydrogen bonds: L:S.473, L:F.476 3PE.15: 18 residues within 4Å: Chain N: W.30, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, L.301, M.316, Y.325, W.326, L.332 Chain Q: H.73 Chain R: R.45, V.49 Ligands: CDL.20 11 PLIP interactions: 9 interactions with chain N, 1 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:W.30, N:W.30, N:L.96, N:V.98, N:L.102, N:Y.103, N:Y.103, N:L.301, N:W.326 Salt bridges: R:R.45 Hydrogen bonds: Q:H.73 3PE.22: 14 residues within 4Å: Chain N: I.320, I.323, I.327, I.334, L.353, A.354, S.357 Chain Q: W.20 Chain R: R.43, E.44, L.47, R.48, V.55, I.59 8 PLIP interactions: 4 interactions with chain N, 3 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:I.323, N:I.327, N:I.334, N:L.353, R:V.55, R:I.59, Q:W.20 Salt bridges: R:R.48

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.2: 23 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, V.66, R.80, H.83, A.87, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:L.51, C:L.51, C:A.87, C:T.126, C:L.133, C:F.179, C:F.183, C:P.186, C:P.186, C:F.187 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.182 HEM.3: 19 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.6 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.98, C:W.113, C:W.113, C:L.119, C:L.120, C:L.197 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.13: 21 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, Y.55, V.66, 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, F.187 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:Q.44, N:I.45, N:L.51, N:L.51, N:Y.55, N:A.87, N:T.126, N:L.133, N:F.179, N:F.183, N:F.187 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.14: 21 residues within 4Å: Chain N: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.17 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:T.112, N:W.113, N:L.119, N:L.120, N:L.197, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:S.205, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

2 x U10: UBIQUINONE-10

U10.5: 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.281, L.294 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.121, C:M.124, C:I.146, C:I.146, C:A.277, C:L.294 U10.16: 12 residues within 4Å: Chain N: F.121, M.124, A.125, F.128, V.145, I.146, P.270, F.274, A.277, Y.278, L.281, L.294 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:F.121, N:M.124, N:A.125, N:I.146, N:I.146, N:A.277, N:L.294

2 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL

UQ6.6: 11 residues within 4Å: Chain C: S.17, F.18, L.21, L.41, M.42, I.45, A.193, I.194, L.197, F.220 Ligands: HEM.3 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.18, C:L.41, C:I.45, C:A.193, C:I.194, C:L.197 Hydrogen bonds: C:S.17 UQ6.17: 11 residues within 4Å: Chain N: S.17, F.18, L.21, L.41, M.42, I.45, I.194, L.197, H.201, F.220 Ligands: HEM.14 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:F.18, N:F.18, N:L.41, N:I.45, N:I.194, N:L.197 Hydrogen bonds: N:H.201

2 x HEC: HEME C

HEC.7: 23 residues within 4Å: Chain D: V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, I.200, R.204, Y.210, L.214, L.215, F.237, P.238, I.242, G.243, M.244, P.247, I.248, V.270, L.274 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:V.120, D:N.189, D:P.194, D:P.195, D:I.200, D:Y.210, D:L.214, D:L.215, D:L.215, D:F.237, D:I.242, D:I.242, D:M.244, D:P.247, D:I.248, D:V.270, D:L.274 Hydrogen bonds: D:Y.210, D:Y.210, D:G.243 Salt bridges: D:R.204 Metal complexes: D:H.125 HEC.18: 21 residues within 4Å: Chain O: V.120, C.121, C.124, H.125, N.189, A.192, P.194, P.195, I.200, R.204, Y.210, L.214, L.215, F.237, I.242, G.243, M.244, P.247, I.248, V.270, L.274 21 PLIP interactions: 21 interactions with chain O, Hydrophobic interactions: O:V.120, O:N.189, O:A.192, O:P.194, O:P.195, O:I.200, O:Y.210, O:L.214, O:L.215, O:L.215, O:F.237, O:I.242, O:M.244, O:P.247, O:I.248, O:V.270, O:L.274 Hydrogen bonds: O:Y.210, O:G.243 Salt bridges: O:R.204 Metal complexes: O:H.125

5 x CDL: CARDIOLIPIN

CDL.8: 10 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Chain F: H.73 Chain G: V.38, R.41, T.42 Ligands: 3PE.4, CDL.9 10 PLIP interactions: 5 interactions with chain C, 3 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: C:W.30, C:F.33 Hydrogen bonds: C:S.29, C:S.29, C:S.29 Salt bridges: G:R.41, G:R.41, G:R.41, F:H.73, F:H.73 CDL.9: 28 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, I.92, L.96, K.227, L.230, G.231, I.234, M.235, I.238 Chain D: L.300, P.301, Y.304, K.307, R.308, K.315 Chain F: R.72, H.73 Chain G: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.8 25 PLIP interactions: 10 interactions with chain D, 9 interactions with chain C, 1 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: D:L.300, D:P.301, D:Y.304, D:Y.304, D:Y.304, D:Y.304, D:Y.304, C:N.32, C:F.33, C:F.33, C:I.92, C:L.96, C:L.230, C:I.234, C:I.234, C:M.235, G:Y.30, G:F.31, G:I.35 Hydrogen bonds: D:Y.304, D:R.308, F:R.72, G:N.37 Salt bridges: D:K.307, G:R.41 CDL.12: 8 residues within 4Å: Chain L: F.370, W.477, L.478, R.479 Chain N: F.18, I.19, H.221 Ligands: 3PE.11 12 PLIP interactions: 7 interactions with chain L, 5 interactions with chain N Hydrophobic interactions: L:L.478, L:L.478, N:F.18, N:F.18, N:I.19, N:I.19 Hydrogen bonds: L:L.478, L:R.479, L:R.479 Salt bridges: L:R.479, L:R.479, N:H.221 CDL.20: 11 residues within 4Å: Chain N: S.28, S.29, W.30, F.33 Chain Q: H.73 Chain R: V.38, R.41, T.42, R.45 Ligands: 3PE.15, CDL.21 8 PLIP interactions: 1 interactions with chain Q, 4 interactions with chain N, 3 interactions with chain R Salt bridges: Q:H.73, R:R.41, R:R.41, R:R.41 Hydrophobic interactions: N:W.30, N:F.33 Hydrogen bonds: N:S.29, N:W.30 CDL.21: 21 residues within 4Å: Chain N: S.29, N.32, F.33, L.36, I.92, K.227, G.231, I.234, I.238 Chain O: L.300, Y.304, K.307, R.308, K.315 Chain R: Y.30, F.31, G.34, I.35, N.37, V.38 Ligands: CDL.20 17 PLIP interactions: 4 interactions with chain R, 7 interactions with chain O, 6 interactions with chain N Hydrophobic interactions: R:Y.30, R:F.31, R:I.35, O:L.300, O:L.300, O:Y.304, O:Y.304, N:F.33, N:F.33, N:L.36, N:I.92, N:I.234, N:I.238 Hydrogen bonds: R:N.37, O:Y.304, O:R.308 Salt bridges: O:K.307

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

PC1.19: 14 residues within 4Å: Chain L: F.476 Chain O: M.306 Chain P: Y.115, T.118, V.125, A.126 Chain U: F.15, R.16, T.18, F.21, A.22, I.25, A.26 Ligands: 3PE.11 10 PLIP interactions: 5 interactions with chain P, 4 interactions with chain U, 1 interactions with chain O Hydrophobic interactions: P:V.125, P:A.126, U:A.22, U:I.25, U:I.25 Hydrogen bonds: P:Y.115, P:T.118 pi-Cation interactions: P:Y.115, U:F.21 Salt bridges: O:K.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y.C. et al., Structural basis of respiratory complex adaptation to cold temperatures. Cell (2024)

Release Date

2024-09-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

L
Aa

B
AB

M
Ab

C
AC

N
Ac

D
AD

O
Ad

E
AE

I
AI

P
Ae

T
Ai

F
AF

Q
Af

G
AG

R
Ag

H
AH

S
Ah

J
AJ

U
Aj

K
AK

V
Ak

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

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

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