SMTL ID : 8ibf.1

Respiratory complex Membrane domain of CI, focus-refined of type II, 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

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

3PE.1: 11 residues within 4Å: Chain B: L.17, A.20, L.21 Chain C: L.14, M.21, F.22, R.23 Chain D: K.585, I.593, I.596 Chain J: V.43 10 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 4 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: C:L.14, C:M.21, B:L.17, B:A.20, B:L.21, D:I.593, D:I.596, J:V.43 Salt bridges: D:K.585, D:K.585 3PE.2: 10 residues within 4Å: Chain D: F.95, F.334, R.456, F.459, G.460, F.463, F.466, V.467 Chain R: W.71 Chain W: L.78 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain R Hydrophobic interactions: D:R.456, D:F.459, D:F.459, D:F.463, D:F.466, D:V.467, R:W.71, R:W.71 3PE.3: 17 residues within 4Å: Chain D: T.166, L.169, Q.170, L.173, Y.174, F.529, I.533, H.534, T.537, P.538, S.541, L.542 Chain E: L.277, M.405 Chain T: N.115, R.116, F.134 15 PLIP interactions: 13 interactions with chain D, 1 interactions with chain E, 1 interactions with chain T Hydrophobic interactions: D:L.173, D:Y.174, D:Y.174, D:F.529, D:F.529, D:I.533, D:T.537, D:T.537, D:P.538, D:L.542, E:L.277, T:F.134 Hydrogen bonds: D:Q.170 Salt bridges: D:H.534, D:H.534 3PE.4: 17 residues within 4Å: Chain D: L.576, T.577, N.579, Q.580, N.594, I.598 Chain F: M.100, P.110, M.156, F.163, M.164, W.167 Chain J: Y.41, S.42, L.45, N.46, Y.61 10 PLIP interactions: 3 interactions with chain D, 4 interactions with chain J, 3 interactions with chain F Hydrophobic interactions: D:I.598, J:L.45, F:P.110, F:F.163, F:W.167 Hydrogen bonds: D:N.579, D:Q.580, J:S.42, J:N.46, J:Y.61 3PE.6: 18 residues within 4Å: Chain A: Y.53 Chain D: I.562, P.563, T.566, S.567, H.570, T.571 Chain E: I.147, F.151, Y.152, I.155, V.212 Chain F: L.170, M.284, M.285, L.288, F.291 Ligands: 3PE.7 13 PLIP interactions: 6 interactions with chain E, 2 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: E:F.151, E:F.151, E:Y.152, E:I.155, E:I.155, E:V.212, F:M.284, F:L.288, D:I.562 Hydrogen bonds: D:S.567, D:S.567, D:T.571, D:T.571 3PE.7: 18 residues within 4Å: Chain E: I.155, P.159, I.162, L.166, H.170, S.191, L.194, L.195, L.197, M.201 Chain F: L.276, I.277, T.280, L.281, M.284 Chain J: E.133, W.135 Ligands: 3PE.6 8 PLIP interactions: 1 interactions with chain J, 3 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: J:W.135, F:L.276, F:I.277, F:L.281, E:I.155, E:L.197 Hydrogen bonds: E:S.191 Salt bridges: E:H.170 3PE.8: 21 residues within 4Å: Chain D: W.66, H.67 Chain E: L.39, P.64, I.67, W.71, I.317, P.371, S.372, P.443, I.445, L.446, L.447, T.449, S.450, K.452, L.453 Chain O: T.101, V.104 Ligands: CDL.5, CDL.14 13 PLIP interactions: 11 interactions with chain E, 1 interactions with chain D, 1 interactions with chain O Hydrophobic interactions: E:L.39, E:I.67, E:W.71, E:W.71, E:I.317, E:P.443, E:L.446, E:L.447, E:L.453, O:V.104 Hydrogen bonds: E:S.450, D:H.67 Salt bridges: E:K.452 3PE.9: 20 residues within 4Å: Chain E: W.16, N.88, L.91, L.94, S.97, M.98, S.101, L.105, M.108, I.127, I.131 Chain F: P.238, A.239, T.242, L.246, P.256 Chain G: N.329 Chain L: M.47 Ligands: CDL.11, 3PE.13 11 PLIP interactions: 6 interactions with chain E, 4 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: E:L.94, E:L.105, E:L.105, E:I.127, E:I.131, F:T.242, F:L.246, F:P.256 Hydrogen bonds: E:N.88, F:T.242, G:N.329 3PE.12: 15 residues within 4Å: Chain D: K.560, T.561, S.565, T.568, L.569, N.572 Chain J: S.109, G.111, T.112, A.114, M.115, G.116, Y.119, M.120 Ligands: 3PE.18 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain D Hydrophobic interactions: J:T.112, J:A.114, J:M.115, J:Y.119, J:Y.119, D:L.569, D:N.572 Hydrogen bonds: J:S.109 Salt bridges: D:K.560 3PE.13: 9 residues within 4Å: Chain E: L.12, W.16, L.17 Chain L: C.40, L.43, V.53, M.54 Ligands: 3PE.9, CDL.11 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.12, E:L.17 3PE.15: 11 residues within 4Å: Chain D: L.9, F.12, I.13, L.16, T.65, W.66 Chain Q: Y.85, H.89, K.93 Ligands: CDL.5, CDL.14 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain Q Hydrophobic interactions: D:L.9, D:L.9, D:L.9, D:F.12, D:I.13, D:L.16, D:T.65, D:W.66, Q:Y.85, Q:Y.85, Q:Y.85, Q:Y.85 Hydrogen bonds: Q:Y.85 Salt bridges: Q:H.89, Q:H.89 3PE.16: 11 residues within 4Å: Chain D: I.180, L.184, L.210, I.211, M.214, I.218 Chain E: N.390, F.391, I.393 Chain U: R.111 Ligands: 3PE.17 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.180, D:L.184, D:L.210, D:I.211, D:M.214, D:I.218, E:N.390, E:F.391 3PE.17: 10 residues within 4Å: Chain E: W.267, F.391, I.394, I.398 Chain U: W.101, V.104, T.107, D.108, R.111 Ligands: 3PE.16 9 PLIP interactions: 4 interactions with chain U, 5 interactions with chain E Hydrophobic interactions: U:W.101, U:V.104, E:W.267, E:F.391, E:F.391, E:I.394, E:I.398 Hydrogen bonds: U:T.107 Salt bridges: U:R.111 3PE.18: 12 residues within 4Å: Chain D: W.557, L.558 Chain J: Y.110, G.111, A.114 Chain U: P.82, T.83, P.84, S.87, G.90, A.91 Ligands: 3PE.12 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain D, 1 interactions with chain U Hydrophobic interactions: J:A.114, D:W.557, D:L.558 Salt bridges: D:K.560 Hydrogen bonds: U:S.87

3 x CDL: CARDIOLIPIN

CDL.5: 30 residues within 4Å: Chain D: L.16, S.22, M.23, R.116, K.119, Y.120, L.123, I.126, T.127, I.130, I.142, M.150, L.153 Chain E: P.353, L.354, T.357, W.358, L.360, M.361, L.364, L.369, P.371, I.445 Chain P: L.68, M.71, K.72, L.75, M.76 Ligands: 3PE.8, 3PE.15 25 PLIP interactions: 10 interactions with chain D, 5 interactions with chain P, 10 interactions with chain E Hydrophobic interactions: D:L.16, D:L.123, D:I.126, D:T.127, D:I.142, P:K.72, P:K.72, P:L.75, P:L.75, P:M.76, E:L.354, E:T.357, E:W.358, E:L.364, E:L.369, E:P.371, E:P.371, E:I.445 Hydrogen bonds: D:Y.120, D:Y.120, E:P.353, E:T.357 Salt bridges: D:K.119, D:K.119, D:K.119 CDL.11: 23 residues within 4Å: Chain E: M.10, M.55, I.120, L.121 Chain F: P.256, M.335, P.338 Chain I: F.169, W.170, T.171, V.172 Chain L: K.25, N.27, P.29, R.30, V.32, Y.33 Chain N: F.22, L.26, K.29, K.33 Ligands: 3PE.9, 3PE.13 14 PLIP interactions: 2 interactions with chain E, 4 interactions with chain I, 2 interactions with chain F, 4 interactions with chain L, 2 interactions with chain N Hydrophobic interactions: E:I.120, E:L.121, I:F.169, I:W.170, I:W.170, I:W.170, F:M.335, F:P.338, L:V.32, L:Y.33, L:Y.33 Salt bridges: L:K.25, N:K.33 Hydrogen bonds: N:K.33 CDL.14: 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.8, 3PE.15 26 PLIP interactions: 8 interactions with chain P, 8 interactions with chain D, 1 interactions with chain X, 5 interactions with chain Q, 1 interactions with chain E, 3 interactions with chain O Hydrophobic interactions: P:V.82, P:I.83, P:I.86, P:T.87, D:W.66, D:W.66, 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, X:R.49, Q:H.89

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.10: 14 residues within 4Å: Chain G: I.66, K.70, N.71, E.88, L.114, Y.118, Q.132, L.135, R.139, E.160, R.161, D.166, F.169, E.226 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:N.71, G:N.71, G:N.71, G:Y.118, G:Y.118, G:Q.132, G:Q.132, G:R.139, G:R.161, G:E.226 Salt bridges: G:K.70, G:K.70

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

EHZ.19: 16 residues within 4Å: Chain H: S.112 Chain V: H.12, V.16, R.47, F.48, H.51, K.52, E.54, M.57, A.60, L.63, L.64, A.67, E.70, F.71, N.74 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain V Hydrogen bonds: H:S.112, V:H.12, V:E.70 Hydrophobic interactions: V:F.71, V:F.71

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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