SMTL ID : 8ibc.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-3-2-2-2-2-2-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.1: 20 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, 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 C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:Y.55, C:A.127, C:L.133, C:F.179, C:F.183, C:P.186, C:F.187 Salt bridges: C:R.80, C:R.80, C:H.83 Metal complexes: C:H.83, C:H.182 HEM.2: 18 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, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.5 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:W.113, C:L.119, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196 HEM.8: 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.87, V.123, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:Q.44, N:I.45, N:L.51, N:Y.55, N:A.127, N:L.133, N:L.133, N:F.179, N:F.183, N:P.186, N:F.187 Hydrogen bonds: N:G.130, N:N.255 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.9: 19 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, F.90, L.94, H.97, V.98, R.100, S.106, W.113, G.116, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.12 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.37, N:F.90, N:L.94, N:W.113, N:L.120, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.35, 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 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine

3PE.3: 12 residues within 4Å: Chain C: W.30, G.99, R.100, Y.103, Y.104, M.316, Y.325, W.326 Chain F: H.73 Chain G: R.41, R.45, V.49 9 PLIP interactions: 3 interactions with chain G, 5 interactions with chain C, 1 interactions with chain F Hydrogen bonds: G:R.41, G:R.41, C:Y.104, F:H.73 Salt bridges: G:R.45 Hydrophobic interactions: C:W.30, C:Y.103, C:Y.103, C:W.326 3PE.10: 17 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, V.49 Ligands: CDL.13 13 PLIP interactions: 12 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: N:W.30, N:W.30, 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 Hydrogen bonds: N:Q.322 Salt bridges: R:R.45

2 x U10: UBIQUINONE-10

U10.4: 9 residues within 4Å: Chain C: F.128, M.129, I.146, L.149, L.150, W.163, I.164, F.181, L.185 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.150, C:W.163, C:I.164, C:F.181, C:F.181, C:F.181, C:L.185 U10.11: 11 residues within 4Å: Chain N: 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 N Hydrophobic interactions: N:F.121, N:M.124, N:A.125, 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

UQ6.5: 13 residues within 4Å: Chain C: S.17, F.18, L.21, W.31, S.35, G.38, L.41, A.190, L.197, S.205, F.220, D.228 Ligands: HEM.2 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.18, C:L.41, C:A.190, C:L.197 Hydrogen bonds: C:S.17, C:D.228 UQ6.12: 8 residues within 4Å: Chain N: S.17, F.18, L.21, M.42, I.194, L.197, F.220 Ligands: HEM.9 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:F.18, N:F.18, N:I.194, N:L.197 Hydrogen bonds: N:S.17

2 x HEC: HEME C

HEC.6: 21 residues within 4Å: Chain D: V.116, 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, I.242, G.243, M.244, P.247, V.270, L.274 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:V.116, D:V.120, D:N.189, D:A.192, D:P.194, D:P.195, D:I.200, D:L.215, D:F.237, D:I.242, D:M.244, D:P.247, D:V.270, D:V.270, D:L.274 Hydrogen bonds: D:Y.210, D:Y.210, D:G.243 Salt bridges: D:R.204 pi-Stacking: D:H.125 Metal complexes: D:H.125 HEC.14: 23 residues within 4Å: Chain O: V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, P.247, V.270, L.274 22 PLIP interactions: 22 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:V.211, O:L.214, O:L.215, O:F.237, O:I.242, O:M.244, O:P.247, O:P.247, O:V.270, O:L.274 Hydrogen bonds: O:L.193, O:Y.210, O:G.243 Salt bridges: O:R.204 pi-Stacking: O:H.125 Metal complexes: O:H.125

3 x CDL: CARDIOLIPIN

CDL.7: 5 residues within 4Å: Chain L: S.473, W.477, L.478 Chain N: H.221, I.229 6 PLIP interactions: 2 interactions with chain N, 4 interactions with chain L Hydrophobic interactions: N:I.229, L:L.478 Salt bridges: N:H.221 Hydrogen bonds: L:S.473, L:F.476, L:L.478 CDL.13: 9 residues within 4Å: Chain N: S.28, S.29, W.30 Chain Q: H.73 Chain R: V.38, R.41, T.42 Ligands: 3PE.10, CDL.15 9 PLIP interactions: 2 interactions with chain Q, 4 interactions with chain R, 3 interactions with chain N Salt bridges: Q:H.73, Q:H.73, R:R.41, R:R.41, R:R.41 Hydrophobic interactions: R:V.38 Hydrogen bonds: N:S.29, N:S.29, N:S.29 CDL.15: 27 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: L.300, P.301, Y.304, K.307, R.308, K.315 Chain Q: R.72, Q.74 Chain R: Y.30, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.13 22 PLIP interactions: 8 interactions with chain N, 4 interactions with chain R, 10 interactions with chain O Hydrophobic interactions: N:N.32, N:F.33, N:F.33, N:I.92, N:L.96, N:L.230, N:I.234, N:M.235, R:Y.30, R:I.35, O:L.300, O:P.301, O:Y.304, O:Y.304, O:Y.304, O:Y.304, O:Y.304 Hydrogen bonds: R:N.37, R:R.41, O:Y.304, O:R.308 Salt bridges: O:K.307

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: EIP
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: JT
Cytochrome b-c1 complex subunit 10: KU

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

F
AF

Q
Af

G
AG

R
Ag

H
AH

S
Ah

J
AJ

T
Aj

K
AK

U
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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