SMTL ID : 6zkb.1

Membrane domain of closed complex I during turnover

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

11 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.1: 22 residues within 4Å: Chain B: D.163, T.166, Q.170, L.173, Y.174, I.177, I.180, G.228, L.229, S.235, Y.529, M.533, H.534, T.537, P.538, N.541 Chain C: I.394, L.398, L.405 Chain U: N.115, R.116, V.117 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.173, B:Y.174, B:I.177, B:L.229, B:T.537, B:P.538, B:P.538, B:N.541, C:I.394, C:L.398, C:L.405 Hydrogen bonds: B:S.235, B:P.530 Salt bridges: B:H.534, B:H.534 3PE.4: 9 residues within 4Å: Chain B: L.378, M.383, L.491, I.495, F.498, I.499, L.502 Chain M: V.64, L.67 6 PLIP interactions: 1 interactions with chain M, 5 interactions with chain B Hydrophobic interactions: M:L.67, B:L.378, B:L.491, B:I.495, B:F.498, B:F.498 3PE.5: 13 residues within 4Å: Chain B: L.562 Chain C: N.188, S.189, W.190, F.194, M.257, P.260, F.261, L.264 Chain E: L.88, L.120, M.127 Ligands: CDL.14 8 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: C:W.190, C:F.194, C:P.260, C:F.261, B:L.562, E:L.88, E:L.120 Hydrogen bonds: C:N.188 3PE.9: 20 residues within 4Å: Chain A: W.43, Q.46, Y.47, Y.53 Chain B: L.562, P.563, S.567, Q.570, M.571 Chain C: N.144, L.147, Y.148, F.151, Y.152, L.212 Chain D: I.284, L.288, Y.291, R.295 Ligands: PC1.6 15 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B, 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: C:Y.148, C:F.151, C:F.151, C:Y.152, C:Y.152, C:L.212, B:L.562, B:P.563, D:I.284, D:L.288, D:Y.291, D:Y.291 Salt bridges: D:R.295 Hydrogen bonds: A:Y.53, A:Y.53 3PE.10: 16 residues within 4Å: Chain D: K.46, S.125, L.128, I.129, T.132, W.133, L.202, I.206, I.209, I.210, T.217, M.220, L.325, M.329 Chain K: P.2 Ligands: 3PE.18 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: D:L.128, D:L.128, D:I.129, D:W.133, D:W.133, D:L.202, D:I.206, D:I.209, D:I.210, D:L.325, K:P.2 Hydrogen bonds: D:K.46, D:K.46, D:S.125 Water bridges: D:R.322 3PE.12: 13 residues within 4Å: Chain D: I.277, L.281 Chain E: L.6, H.7, W.10, L.124, V.125, G.128, Q.129, W.133 Ligands: PC1.6, CDL.13, CDL.14 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:I.277, D:L.281, E:L.6, E:L.124, E:L.124, E:V.125 3PE.18: 10 residues within 4Å: Chain D: Y.143, I.206, I.345, L.346 Chain N: Q.8, L.13, Q.14, F.15, R.80 Ligands: 3PE.10 7 PLIP interactions: 5 interactions with chain N, 2 interactions with chain D Hydrophobic interactions: N:F.15, D:I.206, D:I.345 Hydrogen bonds: N:Q.8, N:L.13, N:F.15 Salt bridges: N:R.80 3PE.19: 12 residues within 4Å: Chain B: W.557 Chain E: Y.108, G.109, A.112 Chain O: P.83, N.84, T.85, S.88, G.91, A.92, I.96 Ligands: CDL.14 7 PLIP interactions: 3 interactions with chain O, 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: O:P.83, O:A.92, O:I.96, B:W.557, B:W.557, B:W.557, E:A.112 3PE.22: 17 residues within 4Å: Chain 0: K.291, P.295, M.302 Chain L: F.8, V.12, E.16, L.19, V.20, S.22, F.23, A.26, G.27 Chain Z: F.96, A.99, L.102, A.103, W.106 11 PLIP interactions: 6 interactions with chain L, 4 interactions with chain Z, 1 interactions with chain 0 Hydrophobic interactions: L:F.8, L:V.12, L:F.23, L:F.23, L:F.23, L:A.26, Z:F.96, Z:A.99, Z:L.102, Z:A.103, 0:P.295 3PE.24: 25 residues within 4Å: Chain 0: M.98, N.99, L.100, F.104, M.108, L.111 Chain 1: L.31, I.34, V.35, G.38, V.39, C.41, G.42, L.45, N.46, S.50, L.54 Chain P: F.140, I.141, W.142, T.144 Chain Y: A.39, H.40 Chain Z: L.3, L.7 11 PLIP interactions: 6 interactions with chain 1, 1 interactions with chain Z, 3 interactions with chain 0, 1 interactions with chain P Hydrophobic interactions: 1:L.31, 1:I.34, 1:V.35, 1:L.45, Z:L.3, 0:L.111 Hydrogen bonds: 1:S.50, 1:S.50, 0:N.99, 0:L.100, P:F.140 3PE.25: 15 residues within 4Å: Chain 1: S.21, K.23, V.88, T.92, G.96, M.99 Chain 2: M.10, T.13, V.14, T.17, M.21, Y.22, R.23 Chain B: K.585, L.596 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain 1, 2 interactions with chain 2 Hydrophobic interactions: B:L.596, 1:V.88, 2:M.21 Salt bridges: B:K.585, 1:K.23, 2:R.23

4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 20 residues within 4Å: Chain B: W.66, H.67, W.68, S.77, L.78, N.136, F.138, I.142 Chain C: P.371, L.449 Chain Q: I.81, Y.84, Y.85, H.89, K.93 Chain V: Q.115, E.116 Ligands: CDL.3, CDL.15, PC1.21 20 PLIP interactions: 9 interactions with chain Q, 8 interactions with chain B, 2 interactions with chain C, 1 interactions with chain V Hydrophobic interactions: Q:I.81, Q:I.81, Q:I.81, Q:Y.84, Q:Y.85, Q:Y.85, Q:H.89, B:W.66, B:W.66, B:W.68, B:W.68, B:L.78, B:F.138, B:I.142, C:P.371, C:P.371 Salt bridges: Q:K.93, Q:K.93, V:E.116 Hydrogen bonds: B:H.67 PC1.6: 23 residues within 4Å: Chain B: I.566 Chain C: A.155, G.156, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Chain D: D.274, I.276, I.277, T.280, I.284 Chain E: L.124, E.131, W.133 Ligands: 3PE.9, 3PE.12, CDL.14 18 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D, 1 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: C:A.155, C:P.159, C:P.159, C:F.194, C:F.194, C:L.197, C:A.198, C:M.201, C:V.205, D:I.276, D:I.277, D:T.280, D:I.284, B:I.566, E:L.124, E:W.133, E:W.133 Hydrogen bonds: D:D.274 PC1.21: 24 residues within 4Å: Chain B: T.16, I.19, W.66, H.67, L.123 Chain C: P.64, I.67, L.68, W.71, I.317, L.446, L.447, L.449, N.450, I.454 Chain V: V.98, G.102, S.103, V.106, A.107, Y.108 Ligands: PC1.2, CDL.3, CDL.15 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:T.16, B:I.19, B:L.123, C:P.64, C:L.68, C:W.71, C:W.71, C:L.446, C:L.447, C:L.447, C:I.454 PC1.23: 21 residues within 4Å: Chain 0: I.175, W.179, P.180, A.182, M.183, F.186, I.187, T.238, I.273, Y.277, F.280, L.288, N.292, F.293, L.296 Chain L: K.15, E.16, A.21, A.24, L.28 Chain P: F.36 21 PLIP interactions: 1 interactions with chain P, 16 interactions with chain 0, 4 interactions with chain L Hydrophobic interactions: P:F.36, 0:I.175, 0:W.179, 0:P.180, 0:A.182, 0:M.183, 0:F.186, 0:F.186, 0:I.187, 0:T.238, 0:I.273, 0:I.273, 0:Y.277, 0:F.280, 0:F.293, 0:L.296, L:A.21, L:A.24, L:L.28 Hydrogen bonds: 0:N.292 Salt bridges: L:E.16

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 39 residues within 4Å: Chain B: N.23, F.24, N.25, L.78, Q.116, K.119, Y.120, L.123, T.127, I.130, Q.139, I.142, M.150 Chain C: P.353, L.354, A.357, W.358, L.360, L.361, L.364, T.365, L.369, P.370, P.371, S.372, L.442, L.445, L.446, S.448, L.449 Chain F: L.68, L.71, I.75 Chain V: L.99, V.100, S.103 Ligands: PC1.2, CDL.15, PC1.21 24 PLIP interactions: 8 interactions with chain C, 2 interactions with chain F, 12 interactions with chain B, 2 interactions with chain V Hydrophobic interactions: C:W.358, C:L.361, C:L.361, C:L.364, C:T.365, C:L.442, C:L.446, F:L.71, F:I.75, B:F.24, B:L.78, B:L.123, B:T.127, B:I.130, B:I.130, B:Q.139, B:I.142, B:I.142, V:L.99, V:L.99 Water bridges: C:A.357 Hydrogen bonds: B:Y.120 Salt bridges: B:K.119, B:K.119 CDL.7: 33 residues within 4Å: Chain C: L.2, I.5, I.6, M.9, M.10, M.12, S.53, T.55, F.56, L.101, L.104, F.105, M.108, F.117, I.120, M.121 Chain D: P.256, L.337, P.338 Chain H: F.169, W.170, T.171, M.172 Chain N: T.29, P.31, R.32, A.34, Y.35, F.38 Chain X: L.27, N.31, K.34 Ligands: CDL.8 34 PLIP interactions: 3 interactions with chain X, 4 interactions with chain H, 14 interactions with chain C, 9 interactions with chain N, 4 interactions with chain D Hydrophobic interactions: X:L.27, H:F.169, H:F.169, C:L.2, C:I.5, C:I.6, C:I.6, C:I.6, C:M.12, C:F.56, C:L.101, C:L.104, C:F.105, C:I.120, N:T.29, N:P.31, N:R.32, N:A.34, N:Y.35, N:Y.35, N:F.38, N:F.38, N:F.38, D:P.256, D:L.337, D:P.338, D:P.338 Hydrogen bonds: X:N.31, X:K.34, H:T.171, H:T.171, C:S.53, C:S.53, C:T.55 CDL.8: 34 residues within 4Å: Chain C: W.16, L.17, A.90, R.91, L.94, M.98, L.101, V.127, I.131, R.135, W.136 Chain D: P.238, I.239, T.241, I.242, L.245, I.246, L.249, L.257, T.334, M.335 Chain J: K.338, Y.339 Chain N: A.34, G.37, F.38, Y.41, C.42, L.45, I.46, A.49, V.55, L.56 Ligands: CDL.7 28 PLIP interactions: 8 interactions with chain D, 6 interactions with chain N, 10 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: D:I.239, D:I.242, D:I.242, D:I.246, D:I.246, D:L.249, D:L.257, N:Y.41, N:Y.41, N:L.45, N:I.46, N:L.56, C:W.16, C:L.17, C:L.94, C:L.101, C:I.131, C:I.131, C:R.135, C:W.136 Water bridges: D:I.239 Hydrogen bonds: N:V.55, C:R.91, J:K.338, J:K.338, J:Y.339 Salt bridges: C:R.135, J:K.338 CDL.11: 22 residues within 4Å: Chain D: M.323, T.324, L.325, T.328, L.332, L.336, L.339 Chain N: I.36, D.47, R.51, R.62, L.65, Y.66, S.69, F.70, F.72, V.73, L.77 Chain W: K.43, L.46, T.47, T.50 19 PLIP interactions: 11 interactions with chain N, 6 interactions with chain D, 2 interactions with chain W Hydrophobic interactions: N:I.36, N:L.65, N:Y.66, N:Y.66, N:F.72, N:F.72, N:V.73, D:L.325, D:L.325, D:L.332, D:L.336, D:L.339, W:T.50 Hydrogen bonds: N:R.51, N:Y.66, N:Y.66, D:L.325 Salt bridges: N:R.62, W:K.43 CDL.13: 38 residues within 4Å: Chain B: T.576, I.577, S.579, Q.580, T.594, S.598, L.601, L.602, F.604 Chain D: P.110, H.112, F.113, L.153, T.156, L.157, L.160, I.164 Chain E: A.2, L.6, Y.9, A.25, I.28, A.31, S.32, V.35, V.36, Y.39, S.40, L.43, K.44, Y.59, A.63, I.66, G.67, F.70, V.125 Ligands: 3PE.12, CDL.14 30 PLIP interactions: 7 interactions with chain B, 7 interactions with chain D, 16 interactions with chain E Hydrophobic interactions: B:I.577, B:L.601, B:L.602, B:L.602, B:F.604, D:P.110, D:F.113, D:L.153, D:T.156, D:L.157, D:L.160, D:I.164, E:L.6, E:Y.9, E:A.25, E:A.31, E:V.35, E:Y.39, E:Y.39, E:A.63, E:I.66, E:F.70, E:F.70, E:F.70, E:V.125 Hydrogen bonds: B:S.579, B:Q.580, E:Y.59 Salt bridges: E:K.44, E:K.44 CDL.14: 24 residues within 4Å: Chain B: T.560, I.561, L.562, T.565, I.566, L.568, A.569, K.572 Chain E: L.101, T.105, G.109, I.110, A.112, A.113, A.114, A.116, Y.117, T.121 Chain O: P.83 Ligands: 3PE.5, PC1.6, 3PE.12, CDL.13, 3PE.19 14 PLIP interactions: 7 interactions with chain E, 7 interactions with chain B Hydrophobic interactions: E:L.101, E:A.112, E:A.113, E:A.113, E:A.114, E:A.116, E:Y.117, B:T.560, B:I.561, B:T.565, B:I.566, B:K.572 Salt bridges: B:K.572, B:K.572 CDL.15: 38 residues within 4Å: Chain B: L.12, I.13, T.16, M.17, A.20, N.65, L.78, F.80, I.126, I.130 Chain F: L.76, G.79, V.82, V.83, I.86, T.87, N.90, V.91, E.95, H.115 Chain I: P.43, V.47, R.48, F.50, I.51, H.55 Chain Q: W.80, I.81, Y.84, Y.85, H.89 Chain V: V.100, T.104, A.107, Y.108 Ligands: PC1.2, CDL.3, PC1.21 36 PLIP interactions: 10 interactions with chain F, 8 interactions with chain Q, 8 interactions with chain I, 7 interactions with chain B, 3 interactions with chain V Hydrophobic interactions: F:L.76, F:V.82, F:V.83, F:V.83, F:I.86, F:I.86, Q:W.80, Q:W.80, Q:W.80, Q:W.80, Q:I.81, Q:Y.84, Q:Y.85, I:P.43, I:V.47, I:V.47, I:F.50, I:I.51, B:L.12, B:I.13, B:T.16, B:A.20, B:L.78, B:I.126, B:I.130, V:V.100, V:Y.108 Hydrogen bonds: F:N.90, F:N.90, F:E.95, I:H.55, V:Y.108 Salt bridges: F:H.115, Q:H.89, I:R.48 Water bridges: I:R.48

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

ZMP.16: 15 residues within 4Å: Chain G: D.112, S.113, L.114 Chain S: H.12, Q.13, V.16, L.44, R.47, F.48, H.51, K.52, A.60, A.67, E.70, F.71 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain S Hydrophobic interactions: G:L.114, S:V.16, S:L.44, S:F.48, S:K.52, S:A.60, S:A.67, S:F.71, S:F.71 Hydrogen bonds: G:S.113, S:Q.13

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.17: 14 residues within 4Å: Chain J: I.66, S.71, E.88, L.114, Y.118, L.131, Q.132, L.135, R.139, R.161, D.166, F.169, E.226, Y.233 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:Y.118, J:Q.132, J:Q.132, J:R.139, J:E.226 Salt bridges: J:K.70, J:R.161 pi-Stacking: J:F.169

1 x MYR: MYRISTIC ACID(Covalent)

MYR.20: 10 residues within 4Å: Chain B: L.413, Y.485, L.486, T.489, V.493 Chain R: G.2, A.3, L.5 Chain U: T.152, Q.154 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain R Hydrophobic interactions: B:L.413, B:V.493, R:L.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kampjut, D. et al., The coupling mechanism of mammalian respiratory complex I. Science (2020)

Release Date

2020-10-07

Peptides

Mitochondrial complex I, 49 kDa subunit: A
NADH-ubiquinone oxidoreductase chain 5: B
NADH-ubiquinone oxidoreductase chain 4: C
NADH-ubiquinone oxidoreductase chain 2: D
Mitochondrial complex I, B14.7 subunit: E
NADH:ubiquinone oxidoreductase subunit B5: F
Acyl carrier protein: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: H
Mitochondrial complex I, PDSW subunit: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: J
NADH:ubiquinone oxidoreductase subunit S5: K
NADH:ubiquinone oxidoreductase subunit A3: L
NADH:ubiquinone oxidoreductase subunit B3: M
NADH dehydrogenase [ubiquinone] 1 subunit C2: N
NADH:ubiquinone oxidoreductase subunit B4: O
Mitochondrial complex I, B16.6 subunit: P
Mitochondrial complex I, B17 subunit: Q
NADH:ubiquinone oxidoreductase subunit B7: R
NADH:ubiquinone oxidoreductase subunit B9: S
NADH:ubiquinone oxidoreductase subunit B2: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: U
Mitochondrial complex I, ESSS subunit: V
Mitochondrial complex I, KFYI subunit: W
Mitochondrial complex I, MNLL subunit: X
Mitochondrial complex I, MWFE subunit: Y
NADH-ubiquinone oxidoreductase chain 3: Z
NADH-ubiquinone oxidoreductase chain 1: 0
NADH-ubiquinone oxidoreductase chain 6: 1
NADH-ubiquinone oxidoreductase chain 4L: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

B
L

C
M

D
N

E
V

F
W

G
X

H
Y

I
Z

J
k

K
l

L
m

M
n

N
o

O
p

P
q

Q
r

R
s

S
t

T
u

U
v

V
w

W
x

X
y

Y
z

Z
A

0
H

1
J

2
K

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial complex I, 49 kDa subunit

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

Mitochondrial complex I, B14.7 subunit

NADH:ubiquinone oxidoreductase subunit B5

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

Mitochondrial complex I, PDSW subunit

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

NADH:ubiquinone oxidoreductase subunit S5

NADH:ubiquinone oxidoreductase subunit A3

NADH:ubiquinone oxidoreductase subunit B3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

Mitochondrial complex I, B16.6 subunit

Mitochondrial complex I, B17 subunit

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

NADH:ubiquinone oxidoreductase subunit B2

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

Mitochondrial complex I, ESSS subunit

Mitochondrial complex I, KFYI subunit

Mitochondrial complex I, MNLL subunit

Mitochondrial complex I, MWFE subunit

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

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