SMTL ID : 8ib6.1

Respiratory complex Membrane domain of CI, focus-refined of type IA, Wild type mouse under cold temperature

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

3PE.1: 6 residues within 4Å: Chain B: W.150, V.153, W.157 Chain F: F.11, L.15 Chain M: I.12 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain B Hydrophobic interactions: F:F.11, F:L.15, B:W.150, B:V.153, B:W.157, B:W.157 3PE.2: 14 residues within 4Å: Chain D: L.9, F.12, I.13, L.16, T.65, W.66, M.78, I.130 Chain Q: Y.84, Y.85, H.89, K.93 Ligands: CDL.6, CDL.17 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain Q Hydrophobic interactions: D:L.9, D:L.9, D:F.12, D:I.13, D:L.16, D:T.65, D:I.130, Q:Y.84, Q:Y.85, Q:Y.85 Salt bridges: Q:H.89, Q:H.89 3PE.3: 15 residues within 4Å: Chain D: K.41, F.44, F.95, W.98, F.334, R.456, F.459, G.460, F.463, A.464, F.466, V.467 Chain R: W.71, R.72 Chain W: L.78 13 PLIP interactions: 2 interactions with chain R, 10 interactions with chain D, 1 interactions with chain W Hydrophobic interactions: R:W.71, R:W.71, D:K.41, D:W.98, D:R.456, D:F.459, D:F.463, D:F.463, D:F.463, D:F.466, D:F.466, D:V.467, W:L.78 3PE.4: 20 residues within 4Å: Chain D: T.166, L.169, Q.170, L.173, Y.174, I.177, F.227, G.228, F.529, H.534, T.537, P.538, S.541, L.542 Chain E: L.277, I.401, M.405 Chain T: N.115, R.116 Ligands: 3PE.5 15 PLIP interactions: 12 interactions with chain D, 2 interactions with chain E, 1 interactions with chain T Hydrophobic interactions: D:L.173, D:Y.174, D:Y.174, D:I.177, D:F.227, D:F.529, D:T.537, D:P.538, D:L.542, E:L.277, E:I.401, T:R.116 Hydrogen bonds: D:Q.170 Salt bridges: D:H.534, D:H.534 3PE.5: 11 residues within 4Å: Chain D: I.180, L.184, I.211, M.214, I.218 Chain E: N.390, I.393, I.401 Chain U: R.111 Ligands: 3PE.4, 3PE.11 8 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D, 1 interactions with chain U Hydrophobic interactions: E:N.390, E:I.393, E:I.401, D:I.180, D:L.184, D:M.214, D:I.218 Salt bridges: U:R.111 3PE.8: 21 residues within 4Å: Chain A: M.52, Y.53 Chain D: I.562, P.563, T.566, S.567, H.570, T.571 Chain E: I.147, Y.148, F.151, Y.152, I.155, V.212 Chain F: L.170, M.284, M.285, L.288, F.291, R.295, Y.298 17 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D, 6 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: E:F.151, E:F.151, E:Y.152, E:I.155, E:I.155, E:V.212, D:I.562, D:I.562, D:T.566, F:M.284, F:L.288, F:L.288, F:F.291, F:F.291, F:F.291 Hydrogen bonds: D:S.567, A:Y.53 3PE.9: 25 residues within 4Å: Chain D: W.66, H.67 Chain E: L.39, L.42, P.64, I.67, W.71, I.317, A.365, P.371, S.372, L.444, I.445, L.446, L.447, T.448, T.449, S.450, K.452, L.453 Chain O: T.101, V.104, A.105 Ligands: CDL.6, CDL.17 17 PLIP interactions: 14 interactions with chain E, 2 interactions with chain O, 1 interactions with chain D Hydrophobic interactions: E:L.39, E:L.42, E:W.71, E:W.71, E:W.71, E:I.317, E:A.365, E:L.444, E:L.446, E:L.447, E:L.453, O:T.101, O:V.104 Hydrogen bonds: E:S.450, D:H.67 Salt bridges: E:K.452, E:K.452 3PE.10: 20 residues within 4Å: Chain E: L.12, W.16, L.91, L.94, S.97, M.98, L.105, I.127, P.128, I.131 Chain F: P.238, A.239, T.242, S.245, L.246, P.256 Chain G: N.329 Chain L: M.47 Ligands: 3PE.13, CDL.15 14 PLIP interactions: 4 interactions with chain F, 10 interactions with chain E Hydrophobic interactions: F:T.242, F:L.246, F:P.256, E:L.12, E:W.16, E:W.16, E:L.94, E:L.94, E:L.105, E:L.105, E:I.127, E:P.128, E:I.131 Hydrogen bonds: F:T.242 3PE.11: 11 residues within 4Å: Chain E: F.391, I.394 Chain U: G.96, P.97, F.100, W.101, Y.103, V.104, T.107, R.111 Ligands: 3PE.5 8 PLIP interactions: 4 interactions with chain U, 4 interactions with chain E Hydrophobic interactions: U:P.97, U:F.100, U:W.101, E:F.391, E:F.391, E:F.391, E:I.394 Hydrogen bonds: U:Y.103 3PE.12: 11 residues within 4Å: Chain E: I.162, L.166, H.170, S.191, A.198 Chain F: L.276, I.277, T.280, L.281, M.284 Chain J: W.135 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: J:W.135, F:I.277, F:T.280, F:L.281, E:A.198 3PE.13: 8 residues within 4Å: Chain E: W.16, L.17, V.90 Chain G: Y.339 Chain L: C.40, V.53, M.54 Ligands: 3PE.10 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain G, 1 interactions with chain E Hydrogen bonds: L:V.53, G:Y.339, G:Y.339 Hydrophobic interactions: E:L.17 3PE.16: 13 residues within 4Å: Chain D: L.576, T.577, Q.580 Chain F: L.157, T.160, M.164 Chain J: C.34, Y.41, S.42, L.45, N.46, Y.61 Ligands: CDL.7 8 PLIP interactions: 5 interactions with chain J, 1 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: J:Y.41, J:L.45, F:L.157, F:T.160 Hydrogen bonds: J:S.42, J:N.46, J:Y.61, D:Q.580

4 x CDL: CARDIOLIPIN

CDL.6: 26 residues within 4Å: Chain D: L.16, S.22, M.23, R.116, K.119, Y.120, L.123, I.126, M.150, L.153 Chain E: P.353, L.354, T.357, W.358, L.360, M.361, L.364, L.369, P.371 Chain P: D.64, L.68, M.71, K.72, L.75 Ligands: 3PE.2, 3PE.9 19 PLIP interactions: 9 interactions with chain D, 7 interactions with chain E, 3 interactions with chain P Hydrophobic interactions: D:L.16, D:L.123, D:L.123, D:I.126, E:T.357, E:W.358, E:L.360, E:L.364, E:L.369, E:P.371, P:K.72, P:L.75, P:L.75 Hydrogen bonds: D:R.116, D:Y.120, E:T.357 Salt bridges: D:K.119, D:K.119, D:K.119 CDL.7: 22 residues within 4Å: Chain D: K.560, T.561, S.565, T.568, L.569, N.572, M.573, L.576 Chain J: G.31, Y.61, T.64, I.68, L.103, T.107, G.111, T.112, A.114, M.115, V.118, Y.119, M.120 Ligands: 3PE.16 15 PLIP interactions: 9 interactions with chain J, 6 interactions with chain D Hydrophobic interactions: J:Y.61, J:T.64, J:I.68, J:L.103, J:T.107, J:A.114, J:V.118, J:V.118, J:Y.119, D:K.560, D:L.576, D:L.576 Hydrogen bonds: D:N.572, D:L.576 Salt bridges: D:K.560 CDL.15: 22 residues within 4Å: Chain E: M.55 Chain F: L.246, P.256, L.257, T.334, M.335, P.338 Chain I: F.169, W.170, T.171, V.172 Chain L: K.25, N.27, D.28, P.29, V.32, Y.33 Chain N: F.22, L.26, K.29, D.30 Ligands: 3PE.10 12 PLIP interactions: 4 interactions with chain F, 3 interactions with chain N, 2 interactions with chain L, 3 interactions with chain I Hydrophobic interactions: F:L.246, F:P.256, F:L.257, F:P.338, N:F.22, L:Y.33, I:F.169, I:W.170, I:W.170 Hydrogen bonds: N:D.30, N:K.33 Salt bridges: L:K.25 CDL.17: 30 residues within 4Å: Chain D: W.66, W.68, L.76, K.77, M.78, N.136, F.138, Q.139, I.142 Chain E: T.449 Chain O: V.98, T.101, T.102, A.105, Y.106 Chain P: V.82, I.83, I.86, T.87, N.90, I.91, E.95, H.115 Chain Q: W.80, F.81, Y.84, H.89 Chain X: R.49 Ligands: 3PE.2, 3PE.9 24 PLIP interactions: 8 interactions with chain P, 6 interactions with chain D, 5 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain X, 3 interactions with chain O Hydrophobic interactions: P:V.82, P:I.83, P:I.86, P:T.87, D:W.66, D:W.68, D:W.68, D:L.76, D:F.138, D:I.142, Q:W.80, Q:F.81, Q:Y.84, Q:Y.84, E:T.449, O:V.98, O:A.105 Hydrogen bonds: P:N.90, P:E.95, P:E.95, O:Y.106 Salt bridges: P:H.115, Q:H.89, X:R.49

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.14: 14 residues within 4Å: Chain G: I.66, C.67, S.68, K.70, L.114, Y.118, Q.132, L.135, R.139, R.161, D.166, F.169, K.221, E.226 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:C.67, G:S.68, G:S.68, G:Y.118, G:Y.118, G:Q.132, G:R.139, G:R.161, G:D.166, G:E.226 Salt bridges: G:K.70 pi-Stacking: G:F.169, G:F.169 pi-Cation interactions: G:R.161

1 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate

EHZ.18: 20 residues within 4Å: Chain H: D.111 Chain V: H.12, Q.13, V.16, L.17, L.19, A.23, H.26, L.27, M.44, R.47, F.48, H.51, K.52, A.60, L.63, A.67, E.70, F.71, N.74 5 PLIP interactions: 5 interactions with chain V Hydrophobic interactions: V:V.16, V:L.27, V:F.71, V:F.71 Hydrogen bonds: V:E.70

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: A
NADH-ubiquinone oxidoreductase chain 6: B
NADH-ubiquinone oxidoreductase chain 4L: C
NADH-ubiquinone oxidoreductase chain 5: D
NADH-ubiquinone oxidoreductase chain 4: E
NADH-ubiquinone oxidoreductase chain 2: F
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: G
Acyl carrier protein, mitochondrial: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: J
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 subunit C2: L
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: M
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: N
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: O
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: P
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: Q
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: S
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: X

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
J

C
K

D
L

E
M

F
N

G
O

H
U

I
X

J
Y

K
c

L
d

M
e

N
f

O
g

P
h

Q
i

R
j

S
k

T
l

U
m

V
n

W
o

X
p

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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