SMTL ID : 8ic4.1

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- 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

9 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.1: 17 residues within 4Å: Chain A: W.43, 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: M.284, L.288, F.291 12 PLIP interactions: 1 interactions with chain A, 3 interactions with chain F, 3 interactions with chain D, 5 interactions with chain E Hydrogen bonds: A:Y.53, D:S.567 Hydrophobic interactions: F:M.284, F:L.288, F:F.291, D:I.562, D:T.566, E:F.151, E:F.151, E:I.155, E:I.155, E:V.212 3PE.2: 3 residues within 4Å: Chain B: W.150, V.153, W.157 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.150, B:W.150, B:V.153, B:W.157 3PE.3: 11 residues within 4Å: Chain D: F.95, F.334, F.459, G.460, F.463, A.464, F.466, V.467 Chain R: F.67, W.71 Chain W: L.78 7 PLIP interactions: 1 interactions with chain W, 2 interactions with chain D, 4 interactions with chain R Hydrophobic interactions: W:L.78, D:F.463, D:F.466, R:F.67, R:F.67, R:W.71, R:W.71 3PE.4: 15 residues within 4Å: Chain D: Q.170, L.173, Y.174, I.177, F.529, I.533, H.534, T.537, P.538, S.541, L.542 Chain T: N.115, R.116, F.134 Ligands: 3PE.9 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain T Hydrophobic interactions: D:L.173, D:L.173, D:Y.174, D:I.177, D:F.529, D:F.529, D:I.533, D:T.537, D:P.538, T:F.134 Hydrogen bonds: D:Q.170, D:Y.174 Salt bridges: D:H.534, D:H.534 3PE.7: 19 residues within 4Å: Chain D: W.66, H.67, W.68 Chain E: L.39, L.42, P.64, I.67, W.71, L.446, L.447, T.449, S.450, K.452, L.453 Chain O: T.101, V.104, A.105 Ligands: CDL.14, 3PE.15 12 PLIP interactions: 1 interactions with chain D, 9 interactions with chain E, 2 interactions with chain O Hydrogen bonds: D:H.67, E:S.450 Hydrophobic interactions: E:L.39, E:L.42, E:W.71, E:W.71, E:W.71, E:L.447, E:L.453, O:T.101, O:V.104 Salt bridges: E:K.452 3PE.8: 13 residues within 4Å: Chain E: I.155, P.159, L.166, H.170, S.191, L.195, L.197, M.201 Chain F: L.276, I.277, T.280, L.281 Chain J: W.135 9 PLIP interactions: 3 interactions with chain F, 2 interactions with chain J, 4 interactions with chain E Hydrophobic interactions: F:L.276, F:I.277, F:T.280, J:W.135, J:W.135, E:I.155, E:P.159, E:M.201 Hydrogen bonds: E:S.191 3PE.9: 10 residues within 4Å: Chain D: I.177 Chain E: N.390, F.391, I.393, I.394, I.398 Chain U: T.107, D.108, R.111 Ligands: 3PE.4 7 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D, 2 interactions with chain U Hydrophobic interactions: E:N.390, E:F.391, E:I.394, E:I.398, D:I.177 Hydrogen bonds: U:T.107 Salt bridges: U:R.111 3PE.15: 15 residues within 4Å: Chain D: L.9, F.12, I.13, T.65, W.66, M.78, F.80 Chain Q: F.81, V.82, Y.84, Y.85, H.89, K.93 Ligands: 3PE.7, CDL.14 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain Q Hydrophobic interactions: D:L.9, D:L.9, D:F.12, D:W.66, D:F.80, Q:F.81, Q:Y.85, Q:Y.85, Q:Y.85, Q:Y.85 Hydrogen bonds: Q:K.93 Salt bridges: Q:H.89, Q:H.89 3PE.16: 14 residues within 4Å: Chain D: W.557, L.558 Chain E: Y.210 Chain J: Y.110, A.114 Chain U: P.82, T.83, P.84, S.87, L.88, G.90, A.91, G.94, F.95 10 PLIP interactions: 1 interactions with chain E, 1 interactions with chain J, 5 interactions with chain D, 3 interactions with chain U Hydrophobic interactions: E:Y.210, D:W.557, D:W.557, D:W.557, D:W.557, D:L.558, U:P.84, U:L.88, U:A.91 Hydrogen bonds: J:Y.110

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 24 residues within 4Å: Chain D: I.19, 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, W.358, L.360, M.361, L.364, P.371, I.445 Chain P: L.68, M.71, K.72, L.75 Ligands: CDL.14 13 PLIP interactions: 5 interactions with chain E, 2 interactions with chain P, 6 interactions with chain D Hydrophobic interactions: E:W.358, E:L.364, E:P.371, E:I.445, P:K.72, P:L.75, 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 CDL.10: 26 residues within 4Å: Chain E: L.6, L.9, P.13, W.16, L.17, V.90, L.94, S.97, M.98, L.105, A.124, I.127, P.128, R.135 Chain F: L.241, T.242, L.246, P.256, M.335 Chain L: L.36, Y.39, C.40, M.47, V.53, M.54 Ligands: CDL.13 14 PLIP interactions: 1 interactions with chain L, 10 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: L:L.36, E:L.6, E:L.9, E:P.13, E:L.17, E:L.94, E:L.105, E:A.124, E:I.127, E:I.127, E:P.128, F:T.242, F:L.246, F:P.256 CDL.12: 23 residues within 4Å: Chain D: L.569, L.576, T.577, Q.580, N.594, L.597, L.601 Chain F: F.113, M.164 Chain J: C.34, G.38, Y.41, S.42, L.45, N.46, R.57, Y.61, I.68, L.103, T.107, T.112, M.120, A.123 16 PLIP interactions: 1 interactions with chain F, 10 interactions with chain J, 5 interactions with chain D Hydrophobic interactions: F:F.113, J:Y.41, J:Y.41, J:Y.41, J:L.45, J:I.68, J:L.103, J:A.123, D:L.569, D:L.597, D:L.597, D:L.601 Hydrogen bonds: J:N.46, J:Y.61, D:Q.580 Salt bridges: J:R.57 CDL.13: 19 residues within 4Å: Chain E: M.55 Chain F: L.257, M.335, P.338 Chain I: W.170, T.171 Chain L: K.25, N.27, P.29, R.30, V.32, Y.33, L.36 Chain N: F.22, L.26, K.29, D.30, K.33 Ligands: CDL.10 9 PLIP interactions: 3 interactions with chain F, 2 interactions with chain I, 2 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: F:L.257, F:M.335, F:P.338, I:W.170, L:Y.33 Hydrogen bonds: I:V.172, N:K.33, N:K.33 Salt bridges: L:K.25 CDL.14: 29 residues within 4Å: Chain D: W.66, W.68, L.76, K.77, M.78, N.136, F.138, I.142 Chain E: T.449 Chain O: 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: CDL.5, 3PE.7, 3PE.15 24 PLIP interactions: 8 interactions with chain D, 5 interactions with chain Q, 8 interactions with chain P, 2 interactions with chain O, 1 interactions with chain X Hydrophobic interactions: 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, P:V.82, P:I.83, P:I.86, P:T.87, O:A.105 Salt bridges: Q:H.89, P:H.115 Hydrogen bonds: P:N.90, P:E.95, P:E.95, O:Y.106, X:R.49

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain D: W.106, H.109, H.348 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.348

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 17 residues within 4Å: Chain G: N.65, I.66, C.67, S.68, K.70, N.71, E.88, F.117, Y.118, L.131, Q.132, L.135, R.139, R.161, F.169, K.221, E.226 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:N.65, G:S.68, G:N.71, 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, G:K.221 pi-Stacking: G:F.117

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

EHZ.17: 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 11 PLIP interactions: 10 interactions with chain V, 1 interactions with chain H Hydrophobic interactions: V:V.16, V:F.48, V:A.67, V:E.70, V:F.71, V:F.71, V:N.74 Hydrogen bonds: V:H.12, V:A.67, 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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