SMTL ID : 7vyi.1

Membrane arm of deactive state CI from Rotenone dataset

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 15 residues within 4Å: Chain C: A.11, E.15, L.18, S.21, F.22, A.23, G.25, I.29 Chain R: A.99, L.102, A.103, W.106 Chain Z: K.291, P.295, M.302 15 PLIP interactions: 8 interactions with chain C, 6 interactions with chain R, 1 interactions with chain Z Hydrophobic interactions: C:A.11, C:L.18, C:F.22, C:F.22, C:F.22, C:A.23, C:I.29, R:A.99, R:L.102, R:A.103, R:W.106, R:W.106 Hydrogen bonds: C:E.15, R:W.106 Salt bridges: Z:K.291 PEE.2: 17 residues within 4Å: Chain C: K.14, V.17, I.24 Chain E: I.9, L.12 Chain Z: I.175, P.180, M.183, F.186, I.187, T.238, I.273, Y.277, L.288, F.293, L.296, W.303 13 PLIP interactions: 2 interactions with chain C, 10 interactions with chain Z, 1 interactions with chain E Hydrophobic interactions: C:I.24, Z:I.175, Z:P.180, Z:F.186, Z:I.187, Z:T.238, Z:I.273, Z:Y.277, Z:Y.277, Z:F.293, Z:W.303, E:I.9 Hydrogen bonds: C:K.14 PEE.6: 16 residues within 4Å: Chain J: I.80, Y.84, H.88 Chain T: W.66, H.67, W.68, S.77, L.78, N.136, F.138, I.142 Chain Y: P.371, L.449 Ligands: CDL.4, PLX.17, CDL.18 10 PLIP interactions: 2 interactions with chain J, 6 interactions with chain T, 2 interactions with chain Y Hydrophobic interactions: J:I.80, T:W.66, T:W.66, T:W.68, T:L.78, T:F.138, T:I.142, Y:P.371, Y:L.449 Salt bridges: J:H.88 PEE.10: 18 residues within 4Å: Chain A: M.19 Chain Q: L.170, M.284, L.287, L.288, Y.291, R.295 Chain T: L.562, P.563, T.566, S.567, Q.570 Chain Y: N.144, L.147, Y.148, F.151, Y.152, A.155 15 PLIP interactions: 3 interactions with chain T, 7 interactions with chain Q, 5 interactions with chain Y Hydrophobic interactions: T:L.562, T:T.566, T:Q.570, Q:L.170, Q:L.288, Q:Y.291, Q:Y.291, Y:L.147, Y:Y.148, Y:F.151, Y:F.151, Y:Y.152 Hydrogen bonds: Q:Y.291, Q:Y.291, Q:R.295 PEE.13: 14 residues within 4Å: Chain K: N.85, R.86 Chain T: T.166, Q.170, L.173, Y.174, L.218, G.228, L.229, M.533, H.534, T.538, N.541 Chain Y: L.405 7 PLIP interactions: 5 interactions with chain T, 1 interactions with chain Y, 1 interactions with chain K Hydrophobic interactions: T:L.173, T:L.218, Y:L.405, K:R.86 Hydrogen bonds: T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.14: 21 residues within 4Å: Chain B: A.39 Chain E: F.109, I.110, Y.112, T.113 Chain R: I.3, M.4, L.7 Chain U: I.34, G.38, G.42, L.45, N.46, S.50, F.57 Chain Z: L.77, M.98, N.99, F.104, M.108, L.111 14 PLIP interactions: 5 interactions with chain Z, 5 interactions with chain U, 1 interactions with chain B, 3 interactions with chain R Hydrophobic interactions: Z:L.77, Z:F.104, Z:L.111, U:I.34, U:L.45, U:L.45, U:F.57, R:I.3, R:I.3, R:L.7 Hydrogen bonds: Z:N.99, Z:L.100, U:S.50, B:A.39 PEE.15: 14 residues within 4Å: Chain D: E.130, W.132 Chain Q: I.276, I.277 Chain Y: A.155, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Ligands: PLX.16 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain Y Hydrophobic interactions: D:W.132, Y:P.159, Y:F.194, Y:F.194, Y:L.197, Y:M.201 Hydrogen bonds: Y:Y.166

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.3: 17 residues within 4Å: Chain F: D.43, S.44, L.45 Chain T: Y.515 Chain X: H.11, Q.12, R.46, F.47, H.50, K.51, A.59, L.62, L.63, A.66, E.69, F.70, G.73 7 PLIP interactions: 5 interactions with chain X, 2 interactions with chain F Hydrophobic interactions: X:F.47, X:A.59, X:F.70 Hydrogen bonds: X:Q.12, X:A.59, F:S.44, F:L.45

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 29 residues within 4Å: Chain I: L.27, I.31, V.33, A.34, I.37, T.38, N.41, H.66 Chain J: W.79, I.80, Y.83, Y.84, H.88 Chain L: V.44, R.48, H.55 Chain M: L.52, V.53, S.56, T.57, A.60, Y.61 Chain T: N.65, F.80 Chain Y: L.442, L.446 Ligands: PEE.6, PLX.17, CDL.18 21 PLIP interactions: 2 interactions with chain Y, 5 interactions with chain J, 8 interactions with chain I, 1 interactions with chain T, 3 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: Y:L.442, Y:L.446, J:W.79, J:W.79, J:I.80, J:Y.84, I:L.27, I:I.31, I:V.33, I:A.34, I:I.37, T:F.80, M:T.57, M:A.60, L:V.44 Salt bridges: J:H.88, I:H.66 Hydrogen bonds: I:N.41, I:N.41, M:Y.61, L:R.48 CDL.8: 22 residues within 4Å: Chain 0: F.168, W.169, T.170, M.171 Chain O: T.28, P.30, R.31, V.33, F.37 Chain Q: P.256, L.335, P.338 Chain V: L.25, R.28, S.29 Chain Y: I.5, I.6, T.9, T.55, F.56, L.121 Ligands: CDL.19 14 PLIP interactions: 2 interactions with chain Q, 4 interactions with chain Y, 2 interactions with chain 0, 4 interactions with chain O, 2 interactions with chain V Hydrophobic interactions: Q:P.256, Q:L.335, Y:I.5, Y:I.6, Y:F.56, Y:L.121, O:V.33, O:V.33, O:F.37, O:F.37, V:L.25 Hydrogen bonds: 0:T.170, 0:T.170, V:L.25 CDL.9: 20 residues within 4Å: Chain 2: P.5, V.9 Chain Q: I.4, Y.6, T.7, T.8, I.10, M.11, M.14, K.46, Q.125, L.128, L.129, T.132, W.133, I.209, L.213, M.217, K.321, L.325 13 PLIP interactions: 13 interactions with chain Q Hydrophobic interactions: Q:I.4, Q:T.7, Q:I.10, Q:L.128, Q:L.129, Q:W.133, Q:I.209, Q:L.213, Q:L.213, Q:L.325 Hydrogen bonds: Q:Y.6, Q:Q.125 Salt bridges: Q:K.46 CDL.12: 19 residues within 4Å: Chain K: G.105, F.106, F.109 Chain T: L.286, L.290, I.293, L.413, I.414, S.417, A.421, R.425, V.493, M.496, L.500, L.504, K.514, S.517, T.519, Y.520 20 PLIP interactions: 14 interactions with chain T, 6 interactions with chain K Hydrophobic interactions: T:L.286, T:L.290, T:I.293, T:L.413, T:A.421, T:V.493, T:L.500, T:L.504, T:T.519, K:F.106, K:F.106, K:F.109, K:F.109, K:F.109, K:F.109 Hydrogen bonds: T:S.517, T:Y.520, T:Y.520 Salt bridges: T:R.425, T:K.514 CDL.18: 29 residues within 4Å: Chain I: L.19 Chain T: T.16, I.19, M.20, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, M.150, L.153 Chain Y: L.354, T.357, W.358, V.361, L.369, P.370, P.371, S.372, L.445, L.446, T.448, L.449 Ligands: CDL.4, PEE.6, PLX.17 22 PLIP interactions: 12 interactions with chain T, 10 interactions with chain Y Hydrophobic interactions: T:T.16, T:L.78, T:L.78, T:L.123, T:I.126, T:I.130, T:L.153, Y:W.358, Y:L.369, Y:P.371, Y:L.445, Y:L.445, Y:L.446, Y:T.448, Y:L.449 Hydrogen bonds: T:Y.120, Y:T.357, Y:T.357 Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119 CDL.19: 32 residues within 4Å: Chain 2: Y.304 Chain O: F.37, Y.40, C.41, L.44, A.48, V.54, V.55 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, L.335 Chain V: W.10 Chain Y: M.10, L.12, P.13, W.16, M.17, T.90, R.91, L.94, M.98, L.101, L.104, F.105, V.127, I.131, R.135 Ligands: CDL.8 21 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain 2, 5 interactions with chain O, 10 interactions with chain Y, 1 interactions with chain V Hydrophobic interactions: Q:L.243, Q:V.246, Q:L.335, O:F.37, O:L.44, O:A.48, O:V.54, Y:L.12, Y:P.13, Y:W.16, Y:W.16, Y:L.94, Y:L.101, Y:L.104, Y:F.105, Y:V.127, Y:I.131, V:W.10 Hydrogen bonds: 2:Y.304, O:V.54 Salt bridges: 2:K.303

5 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.5: 14 residues within 4Å: Chain I: R.74, T.75, F.76, Y.77, D.78 Chain M: L.54, T.57, F.58 Chain V: C.23, R.27 Chain Y: K.3, L.36, I.37, S.40 6 PLIP interactions: 2 interactions with chain I, 1 interactions with chain V, 2 interactions with chain M, 1 interactions with chain Y Hydrophobic interactions: I:F.76, M:F.58, M:F.58, Y:I.37 Salt bridges: I:D.78, V:R.27 PLX.7: 21 residues within 4Å: Chain O: S.4, R.9, P.11, L.12, F.14, M.35, F.72, L.76 Chain P: P.1, F.3 Chain Q: I.202, L.203, I.207, T.210, M.261, L.332, M.339, A.342, L.343, L.346, N.347 13 PLIP interactions: 6 interactions with chain Q, 7 interactions with chain O Hydrophobic interactions: Q:L.203, Q:I.207, Q:T.210, Q:L.332, Q:L.332, Q:A.342, O:F.14, O:F.14, O:F.72, O:F.72, O:L.76 Salt bridges: O:R.9, O:R.79 PLX.11: 9 residues within 4Å: Chain P: L.13 Chain R: N.83, T.86 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 8 PLIP interactions: 6 interactions with chain U, 1 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: U:T.151, U:W.152, U:W.152, U:I.155, U:W.159, P:L.13 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:T.86 PLX.16: 12 residues within 4Å: Chain D: F.90, L.119, A.122 Chain Y: N.188, S.189, W.190, I.193, L.197, M.201, L.212, L.264 Ligands: PEE.15 10 PLIP interactions: 8 interactions with chain Y, 2 interactions with chain D Hydrophobic interactions: Y:W.190, Y:W.190, Y:I.193, Y:L.197, Y:L.212, Y:L.264, D:F.90, D:A.122 pi-Cation interactions: Y:W.190, Y:W.190 PLX.17: 16 residues within 4Å: Chain I: H.66 Chain M: S.56, V.59, A.60, Y.61 Chain T: W.66 Chain Y: L.39, V.67, L.68, W.71, L.446, L.447, N.450 Ligands: CDL.4, PEE.6, CDL.18 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain Y Hydrophobic interactions: M:V.59, Y:L.39, Y:W.71, Y:N.450 Hydrogen bonds: Y:N.450

1 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.20: 13 residues within 4Å: Chain Z: I.11, L.14, L.15, A.18, T.21, R.25, D.51, A.52, L.55, F.56, F.220, F.224, M.225 13 PLIP interactions: 13 interactions with chain Z Hydrophobic interactions: Z:I.11, Z:L.14, Z:L.15, Z:A.18, Z:D.51, Z:L.55, Z:F.56, Z:F.220, Z:F.224, Z:F.224 Hydrogen bonds: Z:T.21, Z:R.25 pi-Stacking: Z:F.224

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

ADP.21: 13 residues within 4Å: Chain 2: I.31, C.32, K.35, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, D.131, F.134, E.191 11 PLIP interactions: 11 interactions with chain 2 Hydrogen bonds: 2:C.32, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:E.191 Salt bridges: 2:K.35, 2:K.35, 2:R.126 pi-Stacking: 2:F.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., The coupling mechanism of mammalian mitochondrial complex I. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-23

Peptides

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: E
Acyl carrier protein, mitochondrial: F
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: G
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: H
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: I
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: L
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: M
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: N
NADH dehydrogenase [ubiquinone] 1 subunit C2: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: P
NADH-ubiquinone oxidoreductase chain 2: Q
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 4L: S
NADH-ubiquinone oxidoreductase chain 5: T
NADH-ubiquinone oxidoreductase chain 6: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: X
NADH-ubiquinone oxidoreductase chain 4: Y
NADH-ubiquinone oxidoreductase chain 1: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
S

C
U

D
V

E
W

F
X

G
Y

H
Z

I
a

J
b

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

Y
r

Z
s

0
u

1
v

2
w

Membrane

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Acyl carrier protein, mitochondrial

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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

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