SMTL ID : 8ic5.1

Respiratory complex CIII2, focus-refined of type I, PERK -/- 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: 22 residues within 4Å: Chain C: 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 C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:Y.55, 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 Metal complexes: C:H.83, C:H.182 HEM.2: 19 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, R.100, S.106, T.112, W.113, G.116, V.117, L.119, H.196, L.200, S.205, N.206 Ligands: UQ6.3 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:T.112, C:W.113, C:V.117, C:L.119, 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 Metal complexes: C:H.97, C:H.196 HEM.7: 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.8: 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: UQ6.11 16 PLIP interactions: 16 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: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: 11 residues within 4Å: Chain C: S.17, F.18, L.21, S.35, G.38, L.41, M.42, A.193, L.197, S.205 Ligands: HEM.2 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.18, C:F.18, C:L.41, C:M.42, C:A.193, C:L.197 Hydrogen bonds: C:S.17, C:S.205 UQ6.11: 11 residues within 4Å: Chain N: S.17, F.18, L.21, A.23, S.35, G.38, M.42, L.197, S.205, F.220 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:F.18, N:L.197 Hydrogen bonds: N:S.17

2 x HEC: HEME C

HEC.4: 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 21 PLIP interactions: 21 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: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.12: 23 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.214, L.215, F.237, P.238, I.242, G.243, M.244, P.247, I.248, V.270, L.274 20 PLIP interactions: 20 interactions with chain O, Hydrophobic interactions: O:V.120, O:N.189, 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

3 x CDL: CARDIOLIPIN

CDL.5: 7 residues within 4Å: Chain L: F.370, W.477, L.478, R.479 Chain N: I.19, H.221 Ligands: 3PE.6 7 PLIP interactions: 2 interactions with chain N, 5 interactions with chain L Hydrophobic interactions: N:I.19, L:L.478 Salt bridges: N:H.221, L:R.479, L:R.479 Hydrogen bonds: L:L.478, L:R.479 CDL.13: 10 residues within 4Å: Chain N: S.28, S.29, W.30 Chain Q: H.73 Chain R: V.38, R.41, T.42, R.45 Ligands: 3PE.9, CDL.14 9 PLIP interactions: 4 interactions with chain N, 4 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:W.30, R:V.38 Hydrogen bonds: N:S.29, N:S.29, N:W.30 Salt bridges: R:R.41, R:R.41, R:R.41, Q:H.73 CDL.14: 19 residues within 4Å: Chain N: S.29, N.32, F.33, I.92, G.231, I.234, I.238 Chain O: Y.304, K.307, R.308, K.315 Chain R: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.13 13 PLIP interactions: 3 interactions with chain O, 5 interactions with chain R, 5 interactions with chain N Hydrogen bonds: O:Y.304, O:R.308, R:N.37, R:R.41 Salt bridges: O:K.307 Hydrophobic interactions: R:Y.30, R:F.31, R:I.35, N:F.33, N:F.33, N:I.92, N:I.234, N:I.238

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

3PE.6: 7 residues within 4Å: Chain L: S.473, F.476, L.478 Chain N: H.221, I.229 Chain O: K.310 Ligands: CDL.5 6 PLIP interactions: 3 interactions with chain N, 2 interactions with chain L, 1 interactions with chain O Hydrophobic interactions: N:I.229 Salt bridges: N:H.221, N:H.221, O:K.310 Hydrogen bonds: L:S.473, L:F.476 3PE.9: 17 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, Y.325, W.326, L.332 Chain Q: H.73 Chain R: R.45, V.49 Ligands: CDL.13 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: N:W.30, N:W.30, N:V.98, N:L.102, N:Y.103, N:Y.104, N:W.326, N:L.332 Salt bridges: R:R.45 3PE.15: 14 residues within 4Å: Chain N: I.320, I.323, I.327, I.334, L.353, A.354 Chain Q: F.17, W.20 Chain R: R.43, E.44, L.47, R.48, V.55, I.59 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain R Hydrophobic interactions: N:I.323, N:I.327, N:I.334, N:L.353, R:V.55, R:I.59 Salt bridges: R:R.48

1 x U10: UBIQUINONE-10

U10.10: 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 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:F.121, N:M.124, N:I.146, N:A.277, N:L.294

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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