SMTL ID : 7vye.1

Membrane arm of deactive state CI from Q10-NADH dataset

Coordinates

PDB Format

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

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

PEE.1: 20 residues within 4Å: Chain C: L.8, A.11, E.15, L.18, V.19, S.21, F.22, A.23, G.25, G.26, I.29 Chain R: I.96, A.99, L.102, A.103, W.106 Chain Z: K.291, P.295, L.298, M.302 17 PLIP interactions: 6 interactions with chain R, 3 interactions with chain Z, 8 interactions with chain C Hydrophobic interactions: R:I.96, R:L.102, R:A.103, R:W.106, R:W.106, Z:P.295, Z:L.298, C:L.8, C:A.11, C:F.22, C:F.22, C:F.22, C:A.23, C:I.29 Hydrogen bonds: R:W.106, C:E.15 Salt bridges: Z:K.291 PEE.2: 8 residues within 4Å: Chain D: I.109, A.112, Y.116, T.120 Chain T: F.568, K.572, M.573 Ligands: CDL.3 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: D:I.109, D:A.112, D:Y.116, T:K.572 Salt bridges: T:K.572, T:K.572 PEE.7: 14 residues within 4Å: Chain J: I.80, Y.84, H.88 Chain T: W.66, H.67, W.68, L.78, F.138, I.142 Chain Y: P.371, L.449 Ligands: CDL.5, CDL.13, PLX.18 12 PLIP interactions: 2 interactions with chain Y, 3 interactions with chain J, 7 interactions with chain T Hydrophobic interactions: Y:P.371, Y:L.449, J:I.80, J:I.80, J:Y.84, T:W.66, T:W.66, T:W.66, T:W.68, T:L.78, T:F.138, T:I.142 PEE.11: 20 residues within 4Å: Chain A: Q.13, M.19, Y.20 Chain Q: L.170, M.284, T.285, L.288, Y.291, R.295 Chain T: L.562, T.566, S.567, Q.570 Chain Y: N.144, L.147, Y.148, F.151, Y.152, A.155 Ligands: PEE.17 17 PLIP interactions: 3 interactions with chain T, 8 interactions with chain Q, 5 interactions with chain Y, 1 interactions with chain A Hydrophobic interactions: T:L.562, T:T.566, T:Q.570, Q:L.170, Q:L.288, 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, A:Q.13 PEE.15: 17 residues within 4Å: Chain K: N.85, R.86 Chain T: D.163, T.166, Q.170, L.173, Y.174, I.177, L.218, L.229, M.533, H.534, T.538, N.541 Chain Y: M.398, M.401, L.405 11 PLIP interactions: 9 interactions with chain T, 1 interactions with chain K, 1 interactions with chain Y Hydrophobic interactions: T:L.173, T:I.177, T:L.218, T:L.229, T:N.541, K:R.86, Y:L.405 Hydrogen bonds: T:D.163, T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.17: 17 residues within 4Å: Chain D: L.123, E.130, W.132 Chain Q: I.276, I.277 Chain T: L.562 Chain Y: A.155, P.159, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Ligands: PEE.11 14 PLIP interactions: 10 interactions with chain Y, 1 interactions with chain T, 2 interactions with chain D, 1 interactions with chain Q Hydrophobic interactions: Y:A.155, Y:P.159, Y:P.159, Y:A.163, Y:F.194, Y:F.194, Y:F.194, Y:L.197, Y:L.197, T:L.562, D:L.123, D:W.132, Q:I.276 Hydrogen bonds: Y:S.191 PEE.19: 17 residues within 4Å: Chain B: A.39 Chain E: F.109, I.110, W.111, Y.112 Chain R: I.3 Chain U: I.34, G.42, L.45, N.46, S.50, L.54, F.57 Chain Z: M.98, N.99, F.104, M.108 10 PLIP interactions: 4 interactions with chain U, 2 interactions with chain R, 3 interactions with chain Z, 1 interactions with chain B Hydrophobic interactions: U:I.34, U:F.57, U:F.57, R:I.3, R:I.3, Z:F.104, Z:F.104 Hydrogen bonds: U:S.50, Z:N.99, B:A.39 PEE.20: 16 residues within 4Å: Chain C: V.17, I.24 Chain E: I.9, L.12 Chain Z: M.183, F.186, I.187, P.197, T.238, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 12 PLIP interactions: 9 interactions with chain Z, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: Z:F.186, Z:F.186, Z:I.187, Z:P.197, Z:T.238, Z:I.273, Z:Y.277, Z:F.293, Z:L.296, E:I.9, E:L.12, C:I.24

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 20 residues within 4Å: Chain D: I.27, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, I.65, G.66, F.69 Chain Q: M.157, L.160, I.164 Chain T: M.576, V.577, Q.580, I.597 Ligands: PEE.2 16 PLIP interactions: 11 interactions with chain D, 2 interactions with chain Q, 3 interactions with chain T Hydrophobic interactions: D:I.27, D:T.31, D:I.34, D:V.35, D:V.35, D:Y.38, D:Y.38, D:L.42, D:I.65, D:F.69, Q:L.160, Q:I.164, T:V.577, T:I.597 Hydrogen bonds: D:Y.58, T:Q.580 CDL.5: 26 residues within 4Å: Chain I: L.27, V.33, A.34, T.38, N.41, V.42, E.46, H.66 Chain J: W.79, I.80, I.81, Y.83, H.88 Chain L: R.42, P.43, A.47, R.48, H.55 Chain M: V.53, S.56, A.60, Y.61 Chain T: T.13, F.80 Ligands: PEE.7, PLX.18 18 PLIP interactions: 5 interactions with chain I, 2 interactions with chain M, 3 interactions with chain L, 7 interactions with chain J, 1 interactions with chain T Hydrophobic interactions: I:L.27, I:V.33, M:V.53, L:P.43, L:A.47, J:W.79, J:W.79, J:I.80, J:Y.83, J:Y.83, J:Y.83, T:F.80 Hydrogen bonds: I:N.41, I:E.46, M:Y.61, L:R.48 Salt bridges: I:H.66, J:H.88 CDL.9: 33 residues within 4Å: Chain 2: Y.304 Chain O: F.37, C.41, L.44, I.45, A.48, V.54, V.55 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, T.334, L.335 Chain V: W.10 Chain Y: M.10, L.12, P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.101, F.105, V.127, I.131, R.135 Ligands: CDL.22 29 PLIP interactions: 12 interactions with chain Y, 9 interactions with chain O, 5 interactions with chain Q, 2 interactions with chain 2, 1 interactions with chain V Hydrophobic interactions: Y:L.12, Y:P.13, Y:W.16, Y:L.94, Y:T.97, Y:L.101, Y:F.105, Y:V.127, Y:I.131, Y:I.131, Y:R.135, O:F.37, O:L.44, O:L.44, O:I.45, O:A.48, O:V.54, O:V.54, O:V.55, Q:V.239, Q:L.243, Q:V.246, Q:T.334, Q:L.335, V:W.10 Hydrogen bonds: Y:T.90, O:V.54, 2:Y.304 Salt bridges: 2:K.303 CDL.10: 19 residues within 4Å: Chain 2: P.5, V.9 Chain Q: P.3, Y.6, T.7, T.8, I.10, M.11, M.14, K.46, Q.125, L.128, L.129, T.132, W.133, L.213, K.321, M.323, L.325 10 PLIP interactions: 10 interactions with chain Q Hydrophobic interactions: Q:Y.6, Q:L.128, Q:L.129, Q:W.133, Q:W.133, Q:L.213, Q:L.325 Hydrogen bonds: Q:Q.125 Salt bridges: Q:K.46, Q:K.321 CDL.13: 25 residues within 4Å: Chain I: L.19 Chain T: I.19, M.20, S.22, N.23, L.78, R.116, K.119, Y.120, L.123, I.130, I.142, G.146, L.153 Chain Y: P.353, L.354, T.357, V.361, L.369, P.371, S.372, L.445, T.448 Ligands: PEE.7, PLX.18 13 PLIP interactions: 4 interactions with chain Y, 9 interactions with chain T Hydrophobic interactions: Y:V.361, Y:T.448, T:L.78, T:L.123, T:I.142, T:L.153 Hydrogen bonds: Y:T.357, Y:T.357, T:Y.120 Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119 CDL.14: 23 residues within 4Å: Chain K: G.105, F.109 Chain T: L.286, I.293, T.294, L.410, M.411, L.413, I.414, S.417, L.418, A.421, R.425, F.429, V.493, M.496, L.500, L.504, K.514, P.516, S.517, T.519, Y.520 22 PLIP interactions: 19 interactions with chain T, 3 interactions with chain K Hydrophobic interactions: T:L.286, T:I.293, T:I.293, T:L.410, T:L.413, T:I.414, T:L.418, T:A.421, T:V.493, T:L.500, T:L.500, T:L.504, T:T.519, K:F.109, K:F.109, K:F.109 Hydrogen bonds: T:S.517, T:S.517, T:Y.520, T:Y.520 Salt bridges: T:R.425, T:K.514 CDL.16: 15 residues within 4Å: Chain D: Y.107, G.108 Chain T: W.557, L.558 Chain W: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97 Chain Y: L.264 10 PLIP interactions: 4 interactions with chain W, 1 interactions with chain Y, 2 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: W:L.87, W:A.90, W:I.94, W:L.97, Y:L.264, T:W.557, T:W.557, T:L.558 Hydrogen bonds: D:Y.107, D:G.108 CDL.22: 23 residues within 4Å: Chain 0: F.168, W.169, T.170, M.171 Chain O: T.28, P.30, R.31, V.33, Y.34, F.37 Chain Q: P.256, L.335, P.338 Chain V: F.21, L.25, R.28, S.29 Chain Y: L.2, I.5, I.6, T.9, F.56 Ligands: CDL.9 15 PLIP interactions: 4 interactions with chain Y, 2 interactions with chain O, 3 interactions with chain 0, 3 interactions with chain Q, 3 interactions with chain V Hydrophobic interactions: Y:L.2, Y:I.5, Y:I.6, Y:F.56, O:V.33, O:F.37, 0:F.168, Q:P.256, Q:L.335, Q:P.338, V:F.21, V:L.25 Hydrogen bonds: 0:T.170, 0:T.170 Salt bridges: V:R.28

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

8Q1.4: 17 residues within 4Å: Chain F: S.44, L.45 Chain T: Y.515 Chain X: H.11, Q.12, R.46, F.47, H.50, K.51, E.53, A.59, L.62, L.63, A.66, E.69, F.70, G.73 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain X Hydrogen bonds: F:S.44, F:L.45, X:A.59 Hydrophobic interactions: X:K.51, X:A.66

4 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.6: 13 residues within 4Å: Chain I: H.60, R.74, T.75, F.76, Y.77, D.78 Chain M: T.57, F.58 Chain V: F.19, C.23 Chain Y: K.3, L.36, S.40 12 PLIP interactions: 2 interactions with chain I, 1 interactions with chain V, 6 interactions with chain Y, 3 interactions with chain M Hydrophobic interactions: I:F.76, V:F.19, Y:K.3, Y:L.36, Y:L.36, M:T.57, M:F.58, M:F.58 Salt bridges: I:D.78, Y:K.3 Hydrogen bonds: Y:S.40, Y:S.40 PLX.8: 23 residues within 4Å: Chain O: S.4, R.9, P.11, L.12, Q.13, F.14, M.35, F.72, L.76, R.79 Chain P: P.1, F.2, F.3 Chain Q: I.202, L.203, L.206, I.207, T.210, L.332, M.339, A.342, L.346, N.347 14 PLIP interactions: 8 interactions with chain Q, 6 interactions with chain O Hydrophobic interactions: Q:L.203, Q:L.206, Q:I.207, Q:L.332, Q:L.332, Q:L.332, Q:M.339, Q:A.342, O:F.72, O:F.72, O:F.72, O:L.76 Salt bridges: O:R.9, O:R.79 PLX.12: 10 residues within 4Å: Chain R: N.83, T.86, M.90, F.93 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 6 PLIP interactions: 4 interactions with chain U, 2 interactions with chain R Hydrophobic interactions: U:T.151, U:W.152, U:W.159, R:F.93 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:T.86 PLX.18: 16 residues within 4Å: Chain M: S.56, V.59, A.60, Y.61 Chain T: M.20, W.66 Chain Y: V.67, L.68, W.71, P.443, L.446, L.447, N.450 Ligands: CDL.5, PEE.7, CDL.13 6 PLIP interactions: 1 interactions with chain M, 5 interactions with chain Y Hydrophobic interactions: M:V.59, Y:W.71, Y:W.71, Y:P.443, Y:L.446 Hydrogen bonds: Y:N.450

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

UQ.21: 12 residues within 4Å: Chain Z: L.14, L.15, A.18, T.21, R.25, D.51, A.52, L.55, F.56, F.220, F.224, M.225 12 PLIP interactions: 12 interactions with chain Z Hydrophobic interactions: Z:L.15, Z:A.18, Z:D.51, Z:A.52, Z:F.56, 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.23: 12 residues within 4Å: Chain 2: I.31, C.32, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, F.134, M.138, E.191 15 PLIP interactions: 15 interactions with chain 2 Hydrogen bonds: 2:C.32, 2:E.53, 2:Y.83, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:E.191, 2:E.191 Salt bridges: 2:K.35, 2:K.35, 2:R.126 pi-Stacking: 2:F.134, 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

2022-12-14

Peptides

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2: 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: F
NADH-ubiquinone oxidoreductase AGGG subunit: G
NADH-ubiquinone oxidoreductase B12 subunit: H
NADH-ubiquinone oxidoreductase SGDH subunit: 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-ubiquinone oxidoreductase KFYI subunit: 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-ubiquinone oxidoreductase B18 subunit: 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

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

NADH-ubiquinone oxidoreductase AGGG subunit

NADH-ubiquinone oxidoreductase B12 subunit

NADH-ubiquinone oxidoreductase SGDH subunit

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-ubiquinone oxidoreductase KFYI subunit

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-ubiquinone oxidoreductase B18 subunit

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

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