SMTL ID : 8iaq.1

Respiratory complex Membrane domain of CI, focused map of type I, Wild type mouse under thermoneutral 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

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

3PE.1: 15 residues within 4Å: Chain B: L.17, A.20, L.21, K.22 Chain C: L.14, L.17, G.18, M.21, F.22, R.23 Chain D: K.585, M.589, L.592, I.593 Chain J: V.43 12 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D, 4 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: B:L.17, B:A.20, B:L.21, B:K.22, D:L.592, D:I.593, C:L.14, C:L.17, C:M.21, J:V.43 Salt bridges: D:K.585, C:R.23 3PE.4: 19 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, I.401, M.405 Chain T: R.116, L.133, F.134, V.137 17 PLIP interactions: 3 interactions with chain E, 11 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: E:L.277, E:I.401, E:I.401, D:L.173, D:F.529, D:F.529, D:I.533, D:T.537, D:P.538, D:L.542, T:L.133, T:F.134, T:V.137 Hydrogen bonds: D:Q.170, D:Q.170 Salt bridges: D:H.534, D:H.534 3PE.6: 20 residues within 4Å: Chain A: W.43, Q.46, 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 11 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:F.151, E:F.151, E:F.151, E:I.155, E:V.212, F:L.170, F:F.291, D:I.562, D:T.566 Hydrogen bonds: D:T.571, A:Q.46 3PE.7: 17 residues within 4Å: Chain E: I.155, P.159, I.162, L.166, H.170, S.191, L.194, L.195, L.197, A.198, M.201 Chain F: L.276, I.277, T.280, L.281 Chain J: E.133, W.135 15 PLIP interactions: 8 interactions with chain E, 4 interactions with chain F, 3 interactions with chain J Hydrophobic interactions: E:I.155, E:P.159, E:I.162, E:L.197, E:A.198, E:M.201, F:L.276, F:I.277, F:T.280, F:L.281, J:W.135, J:W.135 Hydrogen bonds: E:S.191, J:E.133 Salt bridges: E:H.170 3PE.8: 22 residues within 4Å: Chain D: W.66, H.67 Chain E: L.39, L.42, P.64, I.67, W.71, M.361, P.371, S.372, I.445, L.446, L.447, T.449, S.450, K.452, L.453 Chain O: T.101, V.104, A.105 Ligands: CDL.5, CDL.14 16 PLIP interactions: 12 interactions with chain E, 1 interactions with chain D, 3 interactions with chain O Hydrophobic interactions: E:L.39, E:L.42, E:W.71, E:W.71, E:P.371, E:P.371, E:I.445, E:L.446, E:L.447, E:L.453, O:T.101, O:V.104, O:V.104 Hydrogen bonds: E:S.450, D:H.67 Salt bridges: E:K.452 3PE.11: 17 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, V.118, Y.119, M.120 Ligands: CDL.12, 3PE.18 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain D Hydrophobic interactions: J:A.114, J:M.115, J:V.118, J:Y.119, D:T.561, D:L.569 Hydrogen bonds: J:S.109, J:S.109 Salt bridges: D:K.560 3PE.15: 15 residues within 4Å: Chain D: L.9, F.12, I.13, L.16, T.65, W.66, M.78, F.80 Chain Q: F.81, Y.84, Y.85, H.89, K.93 Ligands: CDL.5, CDL.14 13 PLIP interactions: 8 interactions with chain Q, 5 interactions with chain D Hydrophobic interactions: Q:Y.84, Q:Y.85, Q:Y.85, Q:Y.85, D:L.9, D:F.12, D:I.13, D:L.16, D:T.65 Hydrogen bonds: Q:Y.85, Q:H.89 Salt bridges: Q:H.89, Q:H.89 3PE.17: 10 residues within 4Å: Chain E: F.391, I.394 Chain U: G.96, P.97, W.101, Y.103, V.104, T.107, D.108, R.111 8 PLIP interactions: 3 interactions with chain U, 5 interactions with chain E Hydrophobic interactions: U:P.97, U:W.101, E:F.391, E:F.391, E:F.391, E:I.394, E:I.394 Salt bridges: U:R.111 3PE.18: 11 residues within 4Å: Chain D: W.557 Chain J: Y.110, A.114 Chain U: P.82, T.83, P.84, S.87, L.88, G.90, A.91 Ligands: 3PE.11 7 PLIP interactions: 3 interactions with chain U, 3 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: U:P.82, U:L.88, U:A.91, D:W.557, D:W.557, D:W.557, J:A.114

6 x CDL: CARDIOLIPIN

CDL.2: 7 residues within 4Å: Chain B: T.149, W.150, V.153, G.156, W.157 Chain F: F.11, L.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:W.150, B:W.150, B:V.153, B:W.157, F:F.11, F:L.15 CDL.5: 26 residues within 4Å: Chain D: L.16, S.22, M.23, R.116, K.119, Y.120, L.123, T.127, M.150, L.153 Chain E: P.353, L.354, T.357, L.360, M.361, L.364, P.371, I.445 Chain P: L.68, M.71, K.72, L.75, G.79 Ligands: 3PE.8, CDL.14, 3PE.15 18 PLIP interactions: 5 interactions with chain E, 5 interactions with chain P, 8 interactions with chain D Hydrophobic interactions: E:L.364, E:P.371, E:I.445, E:I.445, P:L.68, P:K.72, P:K.72, P:L.75, P:L.75, D:L.16, D:L.123, D:L.123, D:T.127 Hydrogen bonds: E:T.357, D:Y.120 Salt bridges: D:K.119, D:K.119, D:K.119 CDL.9: 24 residues within 4Å: Chain E: I.5, L.9, M.10, M.55, I.104, L.105, L.121 Chain F: P.338 Chain I: W.170, T.171, V.172 Chain L: K.25, N.27, P.29, R.30, V.32, Y.33 Chain N: F.22, Y.25, L.26, K.29, D.30, K.33 Ligands: CDL.13 19 PLIP interactions: 7 interactions with chain L, 5 interactions with chain E, 2 interactions with chain F, 2 interactions with chain N, 3 interactions with chain I Hydrophobic interactions: L:R.30, L:V.32, L:V.32, L:Y.33, L:Y.33, L:Y.33, E:I.5, E:L.9, E:I.104, E:L.105, E:L.121, F:P.338, F:P.338, N:F.22, I:W.170, I:W.170 Salt bridges: L:K.25, N:K.33 Hydrogen bonds: I:V.172 CDL.12: 24 residues within 4Å: Chain D: M.573, L.576, T.577, N.579, N.594, I.598 Chain F: M.100, F.113, I.153, M.156, L.157, I.159, T.160, F.163, M.164, W.167 Chain J: C.34, Y.41, S.42, N.46, Y.61, T.64, T.107 Ligands: 3PE.11 17 PLIP interactions: 8 interactions with chain J, 7 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: J:Y.41, J:Y.41, J:Y.61, J:T.64, F:I.153, F:L.157, F:I.159, F:I.159, F:F.163, F:F.163, F:W.167, D:L.576, D:I.598 Hydrogen bonds: J:S.42, J:N.46, J:Y.61, J:Y.61 CDL.13: 26 residues within 4Å: Chain E: P.13, W.16, L.17, V.90, L.94, S.97, M.98, L.105, I.127, R.135 Chain F: P.238, L.241, T.242, S.245, L.246, P.256, S.301, M.335 Chain G: K.338, Y.339 Chain L: L.36, L.43, M.47, V.53, M.54 Ligands: CDL.9 15 PLIP interactions: 7 interactions with chain E, 1 interactions with chain L, 4 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: E:P.13, E:W.16, E:L.17, E:L.94, E:L.105, E:I.127, L:L.36, F:T.242, F:L.246, F:L.246, F:P.256 Salt bridges: E:R.135 Hydrogen bonds: G:K.338, G:Y.339, G:Y.339 CDL.14: 31 residues within 4Å: Chain D: W.66, W.68, K.77, M.78, N.136, I.142 Chain E: I.442, L.446, T.449 Chain O: L.97, V.98, T.101, T.102, A.105, Y.106 Chain P: V.82, I.86, T.87, N.90, I.91, E.95, H.115 Chain Q: W.80, F.81, Y.84, H.89 Chain X: V.48, R.49 Ligands: CDL.5, 3PE.8, 3PE.15 24 PLIP interactions: 7 interactions with chain P, 6 interactions with chain Q, 5 interactions with chain D, 2 interactions with chain X, 3 interactions with chain O, 1 interactions with chain E Hydrophobic interactions: P:V.82, P:I.86, P:T.87, Q:W.80, Q:F.81, Q:F.81, Q:Y.84, Q:Y.84, D:W.66, D:W.68, D:W.68, D:M.78, D:I.142, X:V.48, O:V.98, O:V.98, E:L.446 Hydrogen bonds: P:N.90, P:N.90, P:E.95, O:Y.106 Salt bridges: P:H.115, Q:H.89, X:R.49

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

PC1.3: 14 residues within 4Å: Chain D: K.41, F.44, I.45, S.91, V.92, F.95, W.98, F.334, K.455, R.456, F.459, G.460 Chain R: Q.57, F.60 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain R Hydrophobic interactions: D:K.41, D:F.44, D:I.45, D:W.98, D:R.456, R:F.60 PC1.16: 11 residues within 4Å: Chain D: F.272, T.275, T.276, C.279, L.280 Chain T: V.141, W.145, H.148, V.149, F.150 Chain W: Y.9 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: D:F.272, D:T.275, D:T.276, D:L.280, T:V.141, T:W.145, T:H.148

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.10: 17 residues within 4Å: Chain G: N.65, I.66, C.67, K.70, E.88, L.114, F.117, Y.118, Q.132, L.135, R.139, R.161, D.166, F.169, K.221, E.226, Y.233 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:Y.118, G:Q.132, G:Q.132, G:R.139, G:E.226 Salt bridges: G:K.70, G:K.70, G:R.161, G:K.221

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: 18 residues within 4Å: Chain H: S.112, L.113 Chain V: H.12, V.16, H.26, M.44, R.47, F.48, H.51, K.52, E.54, M.57, A.60, L.63, A.67, E.70, F.71, N.74 7 PLIP interactions: 6 interactions with chain V, 1 interactions with chain H Hydrophobic interactions: V:V.16, V:F.48, V:A.67, V:F.71, V:F.71 Hydrogen bonds: V:E.70, H:S.112

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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