SMTL ID : 8ib7.1

Respiratory complex CIII2, focus-refined of type IA, 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: 18 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, R.80, H.83, A.84, A.87, A.127, G.130, L.133, P.134, F.179, H.182, F.183, P.186, F.187 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:A.84, 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 pi-Stacking: C:H.83, C:H.83, C:H.182, C:H.182 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, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ6.5 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:V.98, C:W.113, C:L.119, C:L.120, C:L.197, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.12: 20 residues within 4Å: Chain N: Q.44, I.45, G.48, L.51, R.80, H.83, A.84, 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 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:I.45, N:L.51, N:L.51, N:T.126, N:A.127, N:L.133, N:F.179, N:F.183, N:P.186, N:P.186, N:F.187 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.13: 20 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, L.119, L.120, H.196, L.200, S.205, N.206 Ligands: UQ6.16 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:T.112, N:W.113, N:W.113, N:L.119, N:L.120, N:L.200 Hydrogen bonds: N:S.35, N:S.106, N:N.206 Salt bridges: N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

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

3PE.3: 12 residues within 4Å: Chain C: W.30, Y.103, Y.104, M.316, Y.325, W.326 Chain G: V.38, R.41, T.42, R.45, V.49 Ligands: CDL.6 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:W.30, C:Y.103, C:W.326, G:V.38 Hydrogen bonds: C:Y.104, C:Y.325, C:Y.325 Salt bridges: G:R.45 3PE.9: 9 residues within 4Å: Chain C: I.320, I.323, I.327 Chain F: G.16, F.17, W.20 Chain G: L.47, P.51, P.52 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:L.47, G:L.47, G:P.52, C:I.320, C:I.327 3PE.11: 8 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.10 7 PLIP interactions: 5 interactions with chain N, 1 interactions with chain O, 1 interactions with chain L Hydrophobic interactions: N:T.225, N:I.229, L:L.478 Salt bridges: N:H.221, N:H.221, N:H.221, O:K.310 3PE.14: 18 residues within 4Å: Chain N: W.30, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, M.316, Q.322, Y.325, W.326, L.332 Chain Q: H.73 Chain R: R.45, V.49 Ligands: CDL.17 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: N:L.96, N:V.98, N:L.102, N:Y.103, N:Y.103, N:Y.104, N:W.326, N:L.332 Hydrogen bonds: N:Y.104 Salt bridges: R:R.45 3PE.21: 12 residues within 4Å: Chain N: I.320, I.323, I.327 Chain Q: W.20, A.24 Chain R: R.43, E.44, L.47, R.48, P.51, P.52, V.55 10 PLIP interactions: 6 interactions with chain R, 4 interactions with chain N Hydrophobic interactions: R:R.43, R:L.47, R:P.51, R:P.52, R:V.55, N:I.323, N:I.323, N:I.327, N:I.327 Salt bridges: R:R.48

2 x U10: UBIQUINONE-10

U10.4: 10 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 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.121, C:A.125, C:F.128, C:F.128, C:L.294 pi-Stacking: C:F.274 U10.15: 13 residues within 4Å: Chain N: L.118, M.124, A.125, F.128, M.129, I.146, I.164, F.178, F.181, L.185, F.274, A.277, L.294 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:L.118, N:A.125, N:F.128, N:F.128, N:I.164, N:F.178, N:F.178, N:F.181, N:L.185, N:L.185, N:L.294 pi-Stacking: N:F.274

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: 18 residues within 4Å: Chain C: S.17, F.18, L.21, A.23, I.27, S.35, G.38, L.41, M.42, I.45, A.190, A.193, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.2 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.18, C:L.41, C:I.45, C:A.190, C:A.193, C:L.197 Hydrogen bonds: C:H.201, C:H.201, C:S.205 UQ6.16: 15 residues within 4Å: Chain N: S.17, F.18, L.21, A.23, W.31, S.35, G.38, M.42, A.190, A.193, L.197, S.205, F.220, D.228 Ligands: HEM.13 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.18, N:A.190, N:A.193, N:L.197, N:L.197 Hydrogen bonds: N:S.205, N:D.228 pi-Stacking: N:F.220

4 x CDL: CARDIOLIPIN

CDL.6: 15 residues within 4Å: Chain C: S.28, S.29, W.30, N.32, F.33, L.36, I.92, I.234, I.238 Chain D: P.301, Y.304, K.307 Chain F: H.73 Chain G: R.41 Ligands: 3PE.3 11 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 6 interactions with chain C, 3 interactions with chain D Salt bridges: F:H.73, G:R.41, D:K.307 Hydrophobic interactions: C:F.33, C:F.33, C:I.92, C:I.234, D:P.301, D:Y.304 Hydrogen bonds: C:S.29, C:S.29 CDL.10: 9 residues within 4Å: Chain L: F.370, F.476, W.477, L.478, R.479 Chain N: I.19, H.221, T.225 Ligands: 3PE.11 8 PLIP interactions: 5 interactions with chain L, 3 interactions with chain N Hydrophobic interactions: L:L.478, L:R.479, N:T.225 Hydrogen bonds: L:L.478, L:R.479 Salt bridges: L:R.479, N:H.221, N:H.221 CDL.17: 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.14, CDL.20 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.20: 24 residues within 4Å: Chain N: S.29, N.32, F.33, L.36, I.92, L.96, K.227, G.231, I.234, M.235, I.238 Chain O: Y.304, K.307, R.308 Chain Q: R.72, H.73 Chain R: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.17 14 PLIP interactions: 6 interactions with chain N, 4 interactions with chain O, 1 interactions with chain Q, 3 interactions with chain R Hydrophobic interactions: N:F.33, N:F.33, N:I.92, N:L.96, N:I.234, N:M.235, O:Y.304, R:I.35 Hydrogen bonds: O:Y.304, O:R.308, Q:R.72, R:N.37 Salt bridges: O:K.307, R:R.41

2 x HEC: HEME C

HEC.7: 20 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, R.204, L.215, F.237, A.241, I.242, G.243, M.244, P.247, V.270, L.274 18 PLIP interactions: 18 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:L.215, D:I.242, D:I.242, D:M.244, D:P.247, D:V.270, D:V.270, D:L.274 Hydrogen bonds: D:R.204, D:G.243 pi-Cation interactions: D:H.125 Metal complexes: D:H.125 HEC.18: 22 residues within 4Å: Chain O: V.116, V.120, C.121, C.124, H.125, N.189, A.192, P.194, P.195, L.197, I.200, R.204, Y.210, L.214, L.215, F.237, I.242, G.243, M.244, P.247, I.248, V.270 22 PLIP interactions: 22 interactions with chain O, Hydrophobic interactions: O:V.116, O:V.120, O:N.189, O:P.195, O:L.197, O:L.197, O:I.200, O:I.200, O:L.214, O:L.215, O:F.237, O:I.242, O:I.242, O:M.244, O:P.247, O:I.248, O:V.270 Hydrogen bonds: O:Y.210, O:G.243 Salt bridges: O:R.204 pi-Stacking: O:H.125 Metal complexes: O:H.125

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

3PH.8: 16 residues within 4Å: Chain C: V.43, Y.75, M.82, F.236, M.240 Chain D: H.284, M.288, K.291, M.292, M.295, M.296 Chain E: Y.127, A.128, N.131, V.132, Q.135 11 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: E:A.128, E:V.132, D:M.292, D:M.295, C:V.43, C:F.236, C:F.236, C:F.236 Hydrogen bonds: E:N.131 Salt bridges: D:H.284, D:K.291 3PH.19: 16 residues within 4Å: Chain N: V.43, M.82, L.233, F.236, M.240 Chain O: M.288, K.291, M.292, M.295, M.296 Chain P: Y.127, A.128, N.131, V.132, Q.135, F.136 9 PLIP interactions: 2 interactions with chain O, 3 interactions with chain N, 4 interactions with chain P Hydrophobic interactions: O:M.295, N:V.43, N:L.233, N:F.236, P:V.132, P:V.132, P:F.136 Salt bridges: O:K.291 Hydrogen bonds: P:N.131

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.
Show / Hide

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

Related Entries With Identical Sequence