SMTL ID : 7vbp.1

Membrane arm of deactive state CI from DQ-NADH 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(Covalent)(Non-covalent)

PEE.1: 18 residues within 4Å: Chain A: Q.13, Y.20 Chain Q: M.284, T.285, 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, A.155 Ligands: PEE.15 14 PLIP interactions: 4 interactions with chain Y, 4 interactions with chain T, 5 interactions with chain Q, 1 interactions with chain A Hydrophobic interactions: Y:L.147, Y:Y.148, Y:F.151, Y:F.151, T:L.562, T:L.562, T:P.563, T:Q.570, Q:Y.291, Q:Y.291 Hydrogen bonds: Q:Y.291, Q:Y.291, A:Q.13 Salt bridges: Q:R.295 PEE.2: 19 residues within 4Å: Chain C: F.7, L.8, E.15, L.18, V.19, S.21, F.22, A.23, G.25, I.29 Chain R: I.96, A.99, L.102, A.103, W.106, K.109 Chain Z: K.291, P.295, M.302 14 PLIP interactions: 6 interactions with chain R, 1 interactions with chain Z, 7 interactions with chain C Hydrophobic interactions: R:I.96, R:L.102, R:W.106, R:W.106, C:F.7, C:L.8, C:L.18, C:V.19, C:F.22, C:F.22, C:I.29 Hydrogen bonds: R:W.106 Salt bridges: R:K.109, Z:K.291 PEE.7: 14 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 Chain Y: P.371 Ligands: CDL.5, CDL.10, PLX.17 9 PLIP interactions: 3 interactions with chain J, 5 interactions with chain T, 1 interactions with chain Y Hydrophobic interactions: J:I.80, J:Y.84, T:W.66, T:W.66, T:W.68, T:W.68, T:F.138, Y:P.371 Salt bridges: J:H.88 PEE.12: 19 residues within 4Å: Chain K: N.85, R.86 Chain T: D.163, T.166, Q.170, L.173, Y.174, L.217, L.218, G.228, L.229, L.280, Y.529, M.533, H.534, T.538, N.541 Chain Y: M.401, L.405 12 PLIP interactions: 10 interactions with chain T, 1 interactions with chain Y, 1 interactions with chain K Hydrophobic interactions: T:L.173, T:L.217, T:L.218, T:L.229, T:L.280, T:N.541, Y:L.405, K:R.86 Hydrogen bonds: T:D.163, 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 Chain R: I.3, M.4, L.7 Chain U: I.34, V.35, G.38, G.42, L.45, S.50, L.54, F.57 Chain Z: M.98, N.99, L.100, F.104, M.108, L.111 12 PLIP interactions: 2 interactions with chain R, 4 interactions with chain U, 5 interactions with chain Z, 1 interactions with chain E Hydrophobic interactions: R:I.3, R:L.7, U:I.34, U:F.57, Z:F.104, Z:F.104, Z:L.111 Hydrogen bonds: U:S.50, U:S.50, Z:N.99, Z:L.100, E:Y.112 PEE.15: 17 residues within 4Å: Chain D: E.130, W.132 Chain Q: I.276, I.277, T.280, L.281 Chain Y: A.155, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Ligands: PEE.1 11 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain D, 5 interactions with chain Y Hydrophobic interactions: Q:I.276, Q:I.277, Q:L.281, D:W.132, D:W.132, Y:A.163, Y:F.194, Y:A.198, Y:M.201, Y:V.205 Hydrogen bonds: D:E.130 PEE.19: 19 residues within 4Å: Chain C: V.17, I.24 Chain E: I.9 Chain Z: A.182, M.183, M.184, F.186, I.187, P.197, T.238, I.273, Y.277, F.280, H.287, L.288, S.292, F.293, L.296, W.303 15 PLIP interactions: 12 interactions with chain Z, 2 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: Z:F.186, Z:F.186, Z:F.186, Z:I.187, Z:P.197, Z:T.238, Z:I.273, Z:Y.277, Z:F.280, Z:F.293, Z:L.296, Z:W.303, C:I.24, C:I.24, E:I.9

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 14 residues within 4Å: Chain D: Y.107, G.108 Chain T: L.553, W.557, L.558, I.561 Chain W: P.81, P.83, S.86, L.87, A.90, G.93, I.94 Chain Y: L.264 14 PLIP interactions: 6 interactions with chain T, 1 interactions with chain Y, 3 interactions with chain W, 4 interactions with chain D Hydrophobic interactions: T:L.553, T:W.557, T:W.557, T:L.558, T:I.561, T:I.561, Y:L.264, W:L.87, W:A.90, D:Y.107, D:Y.107 Hydrogen bonds: W:S.86, D:Y.107, D:Y.107 CDL.5: 25 residues within 4Å: Chain I: I.26, L.27, G.30, A.34, T.38, N.41, V.42, E.46, H.66 Chain J: W.79, Y.83, Y.84, H.88 Chain L: P.43, A.47, R.48 Chain M: S.56, A.60, Y.61 Chain T: T.13, N.65, F.80 Chain Y: L.446 Ligands: PEE.7, PLX.17 17 PLIP interactions: 1 interactions with chain Y, 6 interactions with chain I, 6 interactions with chain J, 2 interactions with chain L, 1 interactions with chain T, 1 interactions with chain M Hydrophobic interactions: Y:L.446, I:I.26, I:L.27, J:W.79, J:W.79, J:W.79, J:Y.84, J:Y.84, L:A.47, T:F.80 Hydrogen bonds: I:N.41, I:E.46, I:E.46, M:Y.61 Salt bridges: I:H.66, J:H.88, L:R.48 CDL.9: 18 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, P.338 Chain V: F.21, R.28, K.32 Chain Y: M.108, I.120 Ligands: CDL.18 13 PLIP interactions: 3 interactions with chain 0, 5 interactions with chain O, 2 interactions with chain Q, 2 interactions with chain V, 1 interactions with chain Y Hydrophobic interactions: 0:F.168, 0:W.169, O:V.33, O:V.33, O:Y.34, O:F.37, O:F.37, Q:P.256, Q:P.338, Y:I.120 Hydrogen bonds: 0:T.170 Salt bridges: V:K.32, V:K.32 CDL.10: 28 residues within 4Å: Chain I: L.19 Chain T: I.19, M.20, N.23, 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.364, L.369, P.370, P.371, S.372, L.445, L.446, T.448 Ligands: PEE.7, PLX.17 19 PLIP interactions: 8 interactions with chain Y, 11 interactions with chain T Hydrophobic interactions: Y:W.358, Y:L.364, Y:L.369, Y:L.445, Y:L.446, Y:T.448, T:L.123, T:L.123, T:I.126, T:I.130, T:L.153 Hydrogen bonds: Y:T.357, Y:T.357, T:Y.120 Salt bridges: T:K.28, T:R.116, T:K.119, T:K.119, T:K.119 CDL.11: 22 residues within 4Å: Chain K: G.105, F.106, F.109, M.110 Chain T: L.286, I.293, T.294, 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 17 PLIP interactions: 15 interactions with chain T, 2 interactions with chain K Hydrophobic interactions: T:L.286, T:L.410, T:L.413, T:L.413, T:I.414, T:A.421, T:V.493, T:V.493, T:L.500, T:L.500, T:L.504, K:F.106, K:F.109 Hydrogen bonds: T:S.517, T:S.517, T:Y.520 Salt bridges: T:R.425 CDL.18: 34 residues within 4Å: Chain 2: K.303, Y.304 Chain O: F.37, Y.40, C.41, L.44, I.45, A.48, V.54, V.55 Chain Q: P.238, S.242, L.243, M.245, V.246, T.334, L.335 Chain V: L.14 Chain Y: M.10, L.12, P.13, W.16, T.90, R.91, L.94, T.97, M.98, L.101, L.104, F.105, V.127, I.131, R.135 Ligands: CDL.9 28 PLIP interactions: 13 interactions with chain Y, 5 interactions with chain Q, 3 interactions with chain 2, 7 interactions with chain O Hydrophobic interactions: Y:L.12, Y:P.13, Y:W.16, Y:W.16, Y:L.94, Y:L.104, Y:F.105, Y:F.105, Y:V.127, Y:I.131, Y:R.135, Q:L.243, Q:V.246, Q:V.246, Q:T.334, Q:L.335, O:F.37, O:L.44, O:L.44, O:I.45, O:A.48, O:V.54 Hydrogen bonds: Y:T.90, 2:Y.304, 2:Y.304, O:V.54 Salt bridges: Y:R.91, 2:K.303

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

8Q1.4: 19 residues within 4Å: Chain F: D.43, S.44, L.45 Chain X: H.11, Q.12, V.15, A.22, M.43, R.46, F.47, H.50, K.51, A.59, L.62, L.63, A.66, E.69, F.70, G.73 10 PLIP interactions: 7 interactions with chain X, 3 interactions with chain F Hydrophobic interactions: X:A.22, X:R.46, X:F.47, X:F.47, X:A.66, X:F.70, F:L.45 Hydrogen bonds: X:A.59, F:S.44, F:L.45

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: 15 residues within 4Å: Chain I: I.68, R.74, T.75, F.76, Y.77, D.78 Chain M: F.46, L.54, T.57, F.58 Chain V: F.19, R.27 Chain Y: L.36, I.37, S.40 10 PLIP interactions: 2 interactions with chain Y, 4 interactions with chain M, 1 interactions with chain V, 3 interactions with chain I Hydrophobic interactions: Y:L.36, Y:I.37, M:F.46, M:F.46, M:T.57, M:F.58, I:I.68, I:F.76 Hydrogen bonds: V:R.27 Salt bridges: I:D.78 PLX.8: 24 residues within 4Å: Chain O: R.9, P.11, L.12, F.14, 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, M.261, L.332, V.336, M.339, A.342, L.343, S.345, L.346, N.347 13 PLIP interactions: 7 interactions with chain Q, 6 interactions with chain O Hydrophobic interactions: Q:L.203, Q:L.206, Q:I.207, Q:L.332, Q:V.336, Q:M.339, Q:A.342, O:F.14, O:F.72, O:F.72, O:L.76 Salt bridges: O:R.9, O:R.79 PLX.13: 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 7 PLIP interactions: 5 interactions with chain U, 1 interactions with chain R, 1 interactions with chain P Hydrophobic interactions: U:T.151, 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: 15 residues within 4Å: Chain D: L.87, F.90, L.119, A.122 Chain Y: N.188, S.189, W.190, I.193, M.201, G.211, L.212, M.257, P.260, F.261, L.264 10 PLIP interactions: 6 interactions with chain Y, 4 interactions with chain D Hydrophobic interactions: Y:I.193, Y:P.260, Y:F.261, Y:L.264, D:L.87, D:F.90, D:L.119, D:A.122 pi-Cation interactions: Y:W.190, Y:W.190 PLX.17: 21 residues within 4Å: Chain I: H.66 Chain M: V.51, S.56, V.59, A.60, Y.61 Chain T: M.20, N.23, W.66 Chain Y: L.39, V.67, L.68, W.71, P.443, L.446, L.447, L.449, N.450 Ligands: CDL.5, PEE.7, CDL.10 14 PLIP interactions: 2 interactions with chain M, 10 interactions with chain Y, 2 interactions with chain T Hydrophobic interactions: M:V.51, M:V.59, Y:L.39, Y:V.67, Y:L.68, Y:W.71, Y:W.71, Y:P.443, Y:L.447, Y:L.449, Y:N.450, T:M.20, T:N.23 Hydrogen bonds: Y:N.450

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

UQ.20: 12 residues within 4Å: Chain Z: L.14, L.15, A.18, T.21, R.25, P.48, D.51, A.52, L.55, F.220, F.224, M.225 12 PLIP interactions: 12 interactions with chain Z Hydrophobic interactions: Z:L.14, Z:L.15, Z:A.18, Z:D.51, 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(Covalent)

ADP.21: 14 residues within 4Å: Chain 2: I.31, C.32, S.33, K.35, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, D.131, F.134, E.191 13 PLIP interactions: 13 interactions with chain 2 Hydrogen bonds: 2:I.31, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:R.126, 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

2022-04-06

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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