SMTL ID : 8ibg.1

Respiratory complex CIII2, focus-refined of type II, Wild type mouse under cold temperature

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.1: 23 residues within 4Å: Chain C: L.41, 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, Y.131, L.133, P.134, H.182, F.183, P.186, N.255 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:Q.44, C:I.45, C:L.51, C:L.51, C:A.52, C:Y.55, C:A.84, C:T.126, C:L.133, C:F.183, C:P.186, C:P.186 Hydrogen bonds: C:N.255 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.2: 20 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, W.113, G.116, L.119, I.189, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.3 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:W.113, C:W.113, C:W.113, C:L.119, C:L.119, C:I.189, C:L.197 Hydrogen bonds: C:W.31, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Stacking: C:H.196 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196 HEM.6: 22 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, V.123, 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 N, Hydrophobic interactions: N:Q.44, N:I.45, N:L.51, N:L.51, N:Y.55, N:A.84, N:A.127, N:L.133, N:F.179, N:F.183, N:P.186, N:F.187 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.7: 20 residues within 4Å: Chain N: W.31, G.34, L.37, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, V.123, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.10 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:W.113, N:L.119, N:L.120, N:V.123, N:L.197 Hydrogen bonds: N:W.31, N:S.106, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

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

UQ6.3: 14 residues within 4Å: Chain C: S.17, F.18, L.21, W.31, S.35, G.38, L.41, A.190, I.194, L.197, S.205, F.220, D.228 Ligands: HEM.2 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.18, C:F.18, C:L.41, C:A.190, C:I.194, C:L.197 Hydrogen bonds: C:S.17 UQ6.10: 16 residues within 4Å: Chain N: S.17, F.18, L.21, A.23, W.31, S.35, G.38, L.41, M.42, A.190, A.193, L.197, S.205, F.220, D.228 Ligands: HEM.7 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.18, N:L.41, N:A.190, N:A.193, N:L.197, N:L.197 Hydrogen bonds: N:S.17, N:S.205

2 x HEC: HEME C

HEC.4: 21 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, V.211, L.214, L.215, F.237, I.242, G.243, M.244, A.245, P.247 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:V.120, D:N.189, D:A.192, D:P.195, D:I.200, D:V.211, D:L.214, D:L.215, D:F.237, D:M.244, D:A.245, D:P.247 Hydrogen bonds: D:L.193, D:L.193, D:Y.210, D:Y.210 Salt bridges: D:R.204 pi-Stacking: D:H.125 Metal complexes: D:H.125 HEC.11: 19 residues within 4Å: Chain O: 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.215, F.237, G.243, M.244, I.248, V.270, L.274 16 PLIP interactions: 16 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:L.215, O:F.237, O:I.248, O:V.270, O:L.274 Hydrogen bonds: O:L.193, O:Y.210, O:G.243 Salt bridges: O:R.204 Metal complexes: O:H.125

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

3PE.5: 7 residues within 4Å: Chain L: S.473, F.476 Chain N: H.221, T.225, I.229 Chain O: K.310 Chain P: Y.115 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain N Hydrogen bonds: L:S.473 Hydrophobic interactions: N:T.225, N:I.229 Salt bridges: N:H.221, N:H.221 3PE.8: 16 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 Chain Q: H.73 Chain R: R.45 Ligands: CDL.13 11 PLIP interactions: 1 interactions with chain Q, 9 interactions with chain N, 1 interactions with chain R Hydrogen bonds: Q:H.73 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 3PE.15: 13 residues within 4Å: Chain N: P.319, I.320, I.323 Chain Q: F.17, W.20, Y.21 Chain R: R.43, E.44, I.46, L.47, R.48, P.51, P.52 7 PLIP interactions: 5 interactions with chain R, 2 interactions with chain N Hydrophobic interactions: R:R.43, R:I.46, R:L.47, R:P.51, N:I.323, N:I.323 Salt bridges: R:R.48

1 x U10: UBIQUINONE-10

U10.9: 9 residues within 4Å: Chain N: F.121, A.125, F.128, I.146, P.270, F.274, A.277, Y.278, L.294 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:A.125, N:I.146, N:A.277, N:L.294

1 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

3PH.12: 17 residues within 4Å: Chain N: V.43, M.82, F.236, M.240 Chain O: R.287, M.288, K.291, M.292, M.295, M.296, L.299 Chain P: A.128, A.129, N.131, V.132, Q.135 Chain U: D.37 11 PLIP interactions: 4 interactions with chain O, 3 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: O:M.292, O:M.295, O:L.299, P:A.128, P:V.132, N:V.43, N:F.236, N:F.236, N:F.236 Salt bridges: O:K.291 Hydrogen bonds: P:N.131

2 x CDL: CARDIOLIPIN

CDL.13: 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.8, CDL.14 9 PLIP interactions: 1 interactions with chain Q, 4 interactions with chain R, 4 interactions with chain N Salt bridges: Q:H.73, R:R.41, R:R.41, R:R.41 Hydrophobic interactions: R:V.38, N:W.30, N:F.33 Hydrogen bonds: N:S.29, N:S.29 CDL.14: 26 residues within 4Å: Chain N: 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 O: Y.304, K.307, R.308, K.315 Chain Q: R.72, H.73 Chain R: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.13 18 PLIP interactions: 8 interactions with chain N, 3 interactions with chain O, 6 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:N.32, N:F.33, N:F.33, N:I.92, N:L.96, N:I.234, N:I.234, N:M.235, R:Y.30, R:F.31, R:I.35, R:V.38 Hydrogen bonds: O:Y.304, O:R.308, R:N.37, Q:R.72 Salt bridges: O:K.307, R:R.41

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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