SMTL ID : 7vy1.1

Membrane arm of deactive state CI from Q10 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: 14 residues within 4Å: Chain C: V.18, I.25 Chain E: I.40, L.43 Chain Z: M.183, M.184, F.186, I.187, T.238, I.273, Y.277, L.288, F.293, L.296 12 PLIP interactions: 7 interactions with chain Z, 3 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: Z:F.186, Z:F.186, Z:I.187, Z:T.238, Z:I.273, Z:Y.277, Z:F.293, C:I.25, C:I.25, E:I.40, E:L.43 Hydrogen bonds: C:K.15 PEE.3: 20 residues within 4Å: Chain B: A.39 Chain E: F.140, I.141, W.142, Y.143, T.144 Chain R: I.3, M.4, L.7 Chain U: I.34, G.38, G.42, L.45, S.50, L.54, F.57 Chain Z: M.98, N.99, F.104, L.111 12 PLIP interactions: 5 interactions with chain U, 2 interactions with chain R, 4 interactions with chain Z, 1 interactions with chain B Hydrophobic interactions: U:I.34, U:L.45, U:L.54, U:F.57, R:I.3, R:L.7, Z:F.104, Z:F.104, Z:L.111 Hydrogen bonds: U:S.50, Z:N.99, B:A.39 PEE.7: 14 residues within 4Å: Chain J: I.81, Y.85, H.89 Chain T: W.66, H.67, W.68, L.78, F.138, I.142 Chain Y: P.371, L.449 Ligands: CDL.5, PLX.20, CDL.21 10 PLIP interactions: 3 interactions with chain J, 2 interactions with chain Y, 5 interactions with chain T Hydrophobic interactions: J:I.81, J:Y.85, Y:P.371, Y:L.449, T:W.66, T:W.66, T:W.68, T:F.138, T:I.142 Salt bridges: J:K.93 PEE.11: 15 residues within 4Å: Chain A: Y.63 Chain Q: L.170, M.284, L.287, L.288, Y.291, R.295 Chain T: L.562, T.566, S.567, Q.570 Chain Y: N.144, F.151, Y.152, A.155 11 PLIP interactions: 3 interactions with chain T, 6 interactions with chain Q, 2 interactions with chain Y Hydrophobic interactions: T:L.562, T:T.566, T:Q.570, Q:L.170, Q:L.287, Q:Y.291, Q:Y.291, Y:F.151, Y:Y.152 Hydrogen bonds: Q:Y.291 Salt bridges: Q:R.295 PEE.12: 10 residues within 4Å: Chain C: L.9, A.12, L.19, F.23, G.26 Chain R: A.99, A.103, W.106 Chain Z: P.295, M.302 11 PLIP interactions: 4 interactions with chain R, 6 interactions with chain C, 1 interactions with chain Z Hydrophobic interactions: R:A.99, R:W.106, R:W.106, C:L.9, C:A.12, C:F.23, C:F.23, C:F.23, C:F.23 Hydrogen bonds: R:W.106 Salt bridges: Z:K.291 PEE.14: 9 residues within 4Å: Chain D: G.109, I.110, A.113, Y.117, T.121 Chain Q: W.167 Chain T: F.568, K.572, M.573 5 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain T, 1 interactions with chain D Hydrophobic interactions: Q:W.167, T:F.568, T:K.572, D:Y.117 Salt bridges: T:K.572 PEE.16: 12 residues within 4Å: Chain K: N.115, R.116 Chain T: T.166, Q.170, L.173, Y.174, L.229, M.533, H.534, T.538, N.541 Chain Y: L.405 7 PLIP interactions: 1 interactions with chain K, 5 interactions with chain T, 1 interactions with chain Y Hydrophobic interactions: K:R.116, T:L.173, T:L.229, Y:L.405 Hydrogen bonds: T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.18: 15 residues within 4Å: Chain D: L.124, E.131, W.133 Chain Q: I.276, I.277 Chain T: L.562 Chain Y: P.159, Y.166, S.191, F.194, M.195, L.197, A.198, V.205 Ligands: PLX.19 11 PLIP interactions: 6 interactions with chain Y, 2 interactions with chain D, 1 interactions with chain T, 2 interactions with chain Q Hydrophobic interactions: Y:P.159, Y:F.194, Y:L.197, Y:A.198, Y:V.205, D:L.124, D:W.133, T:L.562, Q:I.276, Q:I.277 Hydrogen bonds: Y:S.191

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 22 residues within 4Å: Chain D: T.32, I.35, V.36, Y.39, S.40, L.43, K.44, Y.59, S.63, F.70 Chain Q: P.110, F.113, L.153, M.157, L.160, I.164 Chain T: M.576, Q.580, T.594, I.597, S.598, L.601 17 PLIP interactions: 5 interactions with chain Q, 9 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: Q:P.110, Q:F.113, Q:L.153, Q:L.160, Q:I.164, D:T.32, D:I.35, D:V.36, D:Y.39, D:Y.39, D:Y.39, D:L.43, D:F.70, D:F.70, T:I.597, T:L.601 Hydrogen bonds: T:Q.580 CDL.5: 25 residues within 4Å: Chain I: A.83, I.86, T.87, N.90, E.95, H.115 Chain J: W.80, I.81, Y.84, Y.85, H.89 Chain L: R.43, P.44, R.49, I.52 Chain M: S.103, T.104, A.107, Y.108 Chain T: T.13, N.65, F.80 Ligands: PEE.7, PLX.20, CDL.21 15 PLIP interactions: 5 interactions with chain I, 1 interactions with chain T, 4 interactions with chain J, 3 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: I:A.83, I:I.86, T:F.80, J:W.80, J:I.81, J:Y.85, M:T.104, M:A.107, L:P.44 Hydrogen bonds: I:N.90, I:E.95, M:Y.108, L:R.49 Salt bridges: I:H.115, J:H.89 CDL.9: 31 residues within 4Å: Chain 2: Y.341 Chain O: F.38, C.42, L.45, I.46, A.49, V.55, V.56 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, T.334, L.335 Chain V: V.19 Chain Y: M.10, P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.101, V.127, I.131, R.135 Ligands: CDL.23 21 PLIP interactions: 9 interactions with chain Y, 4 interactions with chain Q, 6 interactions with chain O, 1 interactions with chain V, 1 interactions with chain 2 Hydrophobic interactions: Y:P.13, Y:W.16, Y:W.16, Y:L.94, Y:T.97, Y:L.101, Y:V.127, Y:I.131, Q:L.243, Q:V.246, Q:T.334, Q:L.335, O:F.38, O:L.45, O:I.46, O:A.49, O:V.55, V:V.19 Hydrogen bonds: Y:T.90, O:V.55, 2:Y.341 CDL.10: 18 residues within 4Å: Chain 2: P.42, V.46 Chain Q: 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, L.325 12 PLIP interactions: 12 interactions with chain Q Hydrophobic interactions: Q:Y.6, 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:K.46, Q:Q.125 Salt bridges: Q:K.46 CDL.15: 21 residues within 4Å: Chain K: G.135, F.136, F.139, M.140 Chain T: L.286, I.293, L.410, L.413, I.414, S.417, L.418, A.421, R.425, V.493, M.496, L.500, L.504, P.516, S.517, T.519, Y.520 19 PLIP interactions: 15 interactions with chain T, 4 interactions with chain K Hydrophobic interactions: T:L.286, 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.504, T:T.519, K:F.136, K:F.136, K:F.139, K:F.139 Hydrogen bonds: T:S.517, T:S.517, T:Y.520 Salt bridges: T:R.425 CDL.17: 16 residues within 4Å: Chain D: Y.108 Chain T: L.553, W.557, L.558 Chain W: P.82, T.83, P.84, S.87, L.88, G.90, A.91, G.94, I.95 Chain Y: Y.210, L.264 Ligands: PLX.19 9 PLIP interactions: 2 interactions with chain Y, 3 interactions with chain T, 2 interactions with chain W, 2 interactions with chain D Hydrophobic interactions: Y:Y.210, Y:L.264, T:L.553, T:W.557, T:L.558, W:A.91, W:I.95, D:Y.108 Hydrogen bonds: D:Y.108 CDL.21: 27 residues within 4Å: Chain I: L.68 Chain T: T.16, I.19, M.20, S.22, N.23, Y.27, L.78, R.116, K.119, Y.120, L.123, I.130, L.153 Chain Y: L.354, T.357, W.358, V.361, L.369, P.371, S.372, L.445, T.448, L.449 Ligands: CDL.5, PEE.7, PLX.20 18 PLIP interactions: 9 interactions with chain T, 9 interactions with chain Y Hydrophobic interactions: T:T.16, T:L.78, T:L.123, T:I.130, T:L.153, Y:W.358, Y:L.369, Y:L.445, Y:L.445, Y:L.445, 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 CDL.23: 21 residues within 4Å: Chain 0: F.169, W.170, T.171, M.172 Chain O: T.29, P.31, R.32, V.34, Y.35, F.38 Chain Q: P.256, L.335, P.338 Chain V: F.23, L.27, R.30 Chain Y: L.2, I.6, T.9, T.55 Ligands: CDL.9 13 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain O, 3 interactions with chain Y, 2 interactions with chain V, 2 interactions with chain 0 Hydrophobic interactions: Q:P.256, Q:L.335, Q:P.338, O:V.34, O:Y.35, O:F.38, Y:L.2, Y:I.6, Y:T.55, V:L.27 Salt bridges: V:R.30 Hydrogen bonds: 0:T.171, 0:T.171

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

8Q1.4: 20 residues within 4Å: Chain F: D.111, S.112, L.113 Chain T: F.513, Y.515 Chain X: H.12, Q.13, V.16, M.44, R.47, F.48, H.51, K.52, A.60, L.63, L.64, A.67, E.70, F.71, G.74 6 PLIP interactions: 3 interactions with chain X, 2 interactions with chain F, 1 interactions with chain T Hydrophobic interactions: X:V.16, X:F.48, X:K.52, T:F.513 Hydrogen bonds: F:S.112, F:L.113

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.6: 10 residues within 4Å: Chain I: R.123, T.124, F.125, Y.126, D.127 Chain M: F.105 Chain V: C.25 Chain Y: K.3, L.36, S.40 6 PLIP interactions: 2 interactions with chain I, 3 interactions with chain Y, 1 interactions with chain M Hydrophobic interactions: I:F.125, Y:L.36, M:F.105 Salt bridges: I:D.127, Y:K.3, Y:K.3 PLX.8: 22 residues within 4Å: Chain O: S.5, R.10, P.12, L.13, F.15, F.73, L.77 Chain P: P.2, F.3, F.4 Chain Q: I.202, L.203, L.206, I.207, T.210, M.261, L.332, M.339, A.342, L.343, L.346, N.347 12 PLIP interactions: 7 interactions with chain Q, 5 interactions with chain O Hydrophobic interactions: Q:L.203, Q:L.206, Q:I.207, Q:L.332, Q:L.332, Q:M.339, Q:A.342, O:F.73, O:F.73, O:L.77 Salt bridges: O:R.10, O:R.80 PLX.13: 10 residues within 4Å: Chain P: L.14 Chain R: N.83, T.86, M.90 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 7 PLIP interactions: 1 interactions with chain P, 5 interactions with chain U, 1 interactions with chain R Hydrophobic interactions: P:L.14, U:W.152, U:I.155, U:I.155, U:W.159 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:T.86 PLX.19: 14 residues within 4Å: Chain D: L.120, A.123, M.127 Chain Y: N.188, S.189, W.190, I.193, L.212, Y.256, P.260, F.261, L.264 Ligands: CDL.17, PEE.18 10 PLIP interactions: 8 interactions with chain Y, 2 interactions with chain D Hydrophobic interactions: Y:W.190, Y:I.193, Y:L.212, Y:Y.256, Y:P.260, Y:F.261, Y:L.264, D:L.120, D:A.123 pi-Cation interactions: Y:W.190 PLX.20: 17 residues within 4Å: Chain M: S.103, V.106, A.107, Y.108 Chain T: M.20, N.23, W.66 Chain Y: V.67, L.68, W.71, I.317, L.446, L.447, N.450 Ligands: CDL.5, PEE.7, CDL.21 8 PLIP interactions: 6 interactions with chain Y, 1 interactions with chain T, 1 interactions with chain M Hydrophobic interactions: Y:V.67, Y:W.71, Y:I.317, Y:L.447, Y:N.450, T:N.23, M:V.106 Hydrogen bonds: Y:N.450

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

UQ.22: 11 residues within 4Å: Chain Z: L.14, A.18, T.21, R.25, P.48, D.51, A.52, L.55, F.220, F.224, M.225 9 PLIP interactions: 9 interactions with chain Z Hydrophobic interactions: Z:A.18, Z:A.52, Z:L.55, 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.24: 16 residues within 4Å: Chain 2: N.67, I.68, C.69, S.70, K.72, E.90, L.116, Y.120, L.133, Q.134, L.137, R.141, R.163, D.168, F.171, M.175 12 PLIP interactions: 12 interactions with chain 2 Hydrogen bonds: 2:N.67, 2:C.69, 2:Y.120, 2:Q.134, 2:Q.134, 2:R.141, 2:R.141 Salt bridges: 2:K.72, 2:K.72, 2:R.163 pi-Stacking: 2:F.171, 2:F.171

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: 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 1 beta subcomplex 6: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: L
Complex I-ESSS: M
Complex I-KFYI: N
NADH dehydrogenase [ubiquinone] 1 subunit C2: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: P
NADH-ubiquinone oxidoreductase chain 2: Q
ND3: 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
Complex I-B15: 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

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 1 beta subcomplex 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

Complex I-ESSS

Complex I-KFYI

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 2

ND3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

Complex I-B15

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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