SMTL ID : 6zka.1

Membrane domain of open 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

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

PC1.1: 8 residues within 4Å: Chain A: N.83, T.86, T.89 Chain C: S.148, Y.149, T.151, W.152, I.155 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.89, C:T.151, C:W.152, C:I.155 Hydrogen bonds: A:N.83, A:N.83, A:T.86 PC1.4: 22 residues within 4Å: Chain B: I.175, W.179, P.180, A.182, M.183, F.186, I.187, T.238, I.273, Y.277, F.280, H.287, L.288, N.292, F.293, L.296 Chain O: K.15, E.16, A.24, I.25, L.28 Chain S: F.36 19 PLIP interactions: 13 interactions with chain B, 4 interactions with chain O, 2 interactions with chain S Hydrophobic interactions: B:I.175, B:W.179, B:P.180, B:P.180, B:A.182, B:M.183, B:F.186, B:F.186, B:I.187, B:T.238, B:I.273, B:F.280, B:L.296, O:A.24, O:I.25, O:L.28, S:F.36, S:F.36 Salt bridges: O:E.16 PC1.8: 21 residues within 4Å: Chain E: W.66, H.67, W.68, S.77, L.78, N.136, F.138, I.142 Chain F: P.371, S.448, L.449 Chain T: I.81, Y.84, Y.85, H.89, K.93 Chain Y: Q.115, E.116 Ligands: CDL.9, CDL.19, PC1.28 19 PLIP interactions: 8 interactions with chain T, 9 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: T:I.81, T:Y.84, T:Y.85, T:Y.85, T:H.89, E:W.66, E:W.66, E:W.66, E:W.68, E:W.68, E:L.78, E:F.138, E:I.142, F:P.371, F:P.371 Salt bridges: T:H.89, T:K.93, T:K.93 Hydrogen bonds: E:H.67 PC1.12: 24 residues within 4Å: Chain E: I.566 Chain F: Y.152, A.155, G.156, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Chain G: D.274, I.276, I.277, T.280, L.281, I.284 Chain H: L.124, E.131, W.133 Ligands: 3PE.6, CDL.18 19 PLIP interactions: 5 interactions with chain H, 8 interactions with chain F, 5 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: H:L.124, H:L.124, H:W.133, H:W.133, H:W.133, F:A.155, F:P.159, F:P.159, F:F.194, F:L.197, F:A.198, F:M.201, F:V.205, G:I.277, G:T.280, G:L.281, G:I.284, E:I.566 Hydrogen bonds: G:D.274 PC1.28: 25 residues within 4Å: Chain E: T.16, I.19, W.66, L.123 Chain F: P.64, I.67, L.68, W.71, I.317, L.321, P.443, L.446, L.447, L.449, N.450, I.454 Chain Y: V.98, G.102, S.103, V.106, A.107, Y.108 Ligands: PC1.8, CDL.9, CDL.19 16 PLIP interactions: 1 interactions with chain Y, 12 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: Y:V.98, F:P.64, F:L.68, F:L.68, F:W.71, F:W.71, F:I.317, F:L.321, F:P.443, F:L.446, F:L.447, F:L.449, F:I.454, E:T.16, E:I.19, E:L.123

1 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.2: 9 residues within 4Å: Chain B: T.21, R.25, D.51, A.52, L.55, F.56, F.220, F.224, M.225 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.51, B:A.52, B:L.55, B:F.224, B:F.224 Hydrogen bonds: B:R.25, B:D.51

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

3PE.3: 27 residues within 4Å: Chain 1: A.39 Chain A: L.3, M.4, L.7, F.11 Chain B: L.77, T.80, L.81, M.98, N.99, L.100, F.104, M.108 Chain C: I.34, G.38, V.39, G.42, L.45, N.46, S.50, L.54, F.57 Chain S: F.140, I.141, W.142, Y.143, T.144 17 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A, 7 interactions with chain B, 1 interactions with chain S Hydrophobic interactions: C:I.34, C:V.39, C:L.54, C:F.57, C:F.57, A:L.3, A:L.7, A:F.11, B:L.77, B:T.80, B:L.81, B:F.104, B:F.104 Hydrogen bonds: C:S.50, B:N.99, B:L.100, S:Y.143 3PE.5: 15 residues within 4Å: Chain C: S.21, K.23, V.88, T.92, G.96 Chain D: V.14, T.17, G.18, M.21, Y.22, R.23 Chain E: K.585, L.592, L.596 Ligands: 3PE.15 11 PLIP interactions: 5 interactions with chain D, 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: D:V.14, D:V.14, D:M.21, E:L.592, E:L.596, E:L.596, C:T.92 Hydrogen bonds: D:R.23 Salt bridges: D:R.23, E:K.585, C:K.23 3PE.6: 20 residues within 4Å: Chain 2: W.43, Q.46, Y.47, M.52, Y.53 Chain E: P.563, I.566, S.567, Q.570, M.571 Chain F: N.144, L.147, Y.148, F.151, Y.152 Chain G: I.284, L.288, Y.291 Ligands: PC1.12, CDL.18 14 PLIP interactions: 6 interactions with chain G, 4 interactions with chain F, 2 interactions with chain E, 2 interactions with chain 2 Hydrophobic interactions: G:I.284, G:L.288, G:Y.291, G:Y.291, G:Y.291, G:Y.291, F:Y.148, F:F.151, F:Y.152, E:P.563, E:I.566 Hydrogen bonds: F:N.144, 2:Q.46, 2:Y.53 3PE.7: 24 residues within 4Å: Chain E: D.163, T.166, Q.170, L.173, Y.174, I.177, I.180, I.217, L.218, T.221, F.227, G.228, L.229, Y.529, M.533, H.534, T.537, P.538, N.541 Chain F: L.405 Chain X: R.114, N.115, R.116, V.117 17 PLIP interactions: 15 interactions with chain E, 1 interactions with chain F, 1 interactions with chain X Hydrophobic interactions: E:L.173, E:Y.174, E:I.177, E:I.217, E:T.221, E:L.229, E:T.537, E:P.538, E:N.541, F:L.405, X:R.116 Hydrogen bonds: E:D.163, E:D.163 Water bridges: E:Q.170, E:H.534 Salt bridges: E:H.534, E:H.534 3PE.10: 7 residues within 4Å: Chain E: L.378, M.383, F.498, I.499, L.502 Chain P: V.64, L.67 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain P Hydrophobic interactions: E:L.378, E:F.498, E:F.498, E:F.498, P:V.64, P:L.67 3PE.11: 19 residues within 4Å: Chain E: L.558, I.561, L.562 Chain F: N.188, W.190, F.194, M.201, L.209, Y.210, G.211, L.212, F.256, M.257, P.260, F.261, L.264 Chain H: L.88, M.127 Ligands: CDL.18 12 PLIP interactions: 8 interactions with chain F, 1 interactions with chain H, 3 interactions with chain E Hydrophobic interactions: F:W.190, F:F.194, F:L.209, F:L.212, F:P.260, F:F.261, F:L.264, H:L.88, E:L.558, E:I.561, E:L.562 Hydrogen bonds: F:N.188 3PE.14: 18 residues within 4Å: Chain G: L.10, K.46, S.125, L.128, I.129, T.132, W.133, L.136, I.206, I.209, I.210, S.213, T.217, M.220, R.322, T.324, M.329 Chain N: F.4 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain N Hydrophobic interactions: G:L.10, G:L.128, G:L.128, G:I.129, G:W.133, G:I.206, G:I.210, G:T.217, N:F.4 Hydrogen bonds: G:S.125 Water bridges: G:K.46 Salt bridges: G:K.46 3PE.15: 12 residues within 4Å: Chain E: L.589, I.593 Chain H: L.34, A.38, V.41, P.46, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.5 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain E Hydrophobic interactions: H:L.34, H:A.38, H:V.41, H:F.49, H:F.49, H:V.53, H:T.56, E:L.589, E:I.593 3PE.16: 11 residues within 4Å: Chain G: I.277 Chain H: L.6, H.7, W.10, L.124, V.125, G.128, Q.129, W.133 Ligands: CDL.17, CDL.18 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:L.6, G:I.277 Salt bridges: H:K.134 3PE.23: 15 residues within 4Å: Chain A: F.96, A.99, L.102, A.103, W.106 Chain B: P.295, M.302 Chain O: E.16, L.19, V.20, S.22, F.23, A.24, A.26, G.27 11 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 4 interactions with chain O Hydrophobic interactions: A:F.96, A:A.99, A:L.102, A:A.103, A:W.106, B:P.295, O:F.23, O:F.23, O:A.26 Salt bridges: B:K.291 Hydrogen bonds: O:E.16 3PE.24: 10 residues within 4Å: Chain G: Y.143, I.345 Chain N: P.2 Chain Q: Q.8, P.12, L.13, Q.14, F.15, R.80 Ligands: CDL.25 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain G Hydrophobic interactions: Q:F.15 Hydrogen bonds: Q:Q.8, Q:L.13, Q:Q.14, Q:F.15, Q:R.80, G:Y.143 Water bridges: Q:R.80 Salt bridges: Q:R.80 3PE.26: 12 residues within 4Å: Chain E: W.557, L.558 Chain H: Y.108, G.109, A.112 Chain R: P.83, N.84, T.85, S.88, G.91, A.92 Ligands: CDL.18 8 PLIP interactions: 4 interactions with chain E, 3 interactions with chain R, 1 interactions with chain H Hydrophobic interactions: E:W.557, E:W.557, E:W.557, E:L.558, R:P.83, H:A.112 Hydrogen bonds: R:P.83, R:T.85

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 35 residues within 4Å: Chain E: N.23, F.24, L.78, Q.116, K.119, Y.120, L.123, T.127, I.130, I.142, M.150 Chain F: P.353, L.354, A.357, W.358, L.360, L.361, L.364, L.369, P.370, P.371, S.372, L.442, L.445, L.446, S.448, L.449 Chain I: L.68, L.71, R.72, I.75 Chain Y: L.99 Ligands: PC1.8, CDL.19, PC1.28 30 PLIP interactions: 2 interactions with chain Y, 12 interactions with chain E, 3 interactions with chain I, 13 interactions with chain F Hydrophobic interactions: Y:L.99, Y:L.99, E:F.24, E:L.78, E:T.127, E:I.130, E:I.130, E:I.142, E:I.142, I:L.71, I:R.72, I:I.75, F:W.358, F:W.358, F:L.361, F:L.361, F:L.364, F:L.364, F:L.369, F:P.371, F:L.442, F:L.442, F:L.445, F:L.445, F:L.449 Hydrogen bonds: E:N.23, E:Q.116, E:Y.120 Salt bridges: E:K.119, E:K.119 CDL.13: 33 residues within 4Å: Chain F: W.16, N.88, A.90, R.91, L.94, M.98, L.101, V.127, I.131, R.135 Chain G: P.238, I.239, T.241, I.242, L.245, I.246, L.249, L.257, T.334, M.335 Chain M: Q.329, K.338, Y.339 Chain Q: A.34, G.37, F.38, Y.41, C.42, L.45, I.46, A.49, V.55, L.56 33 PLIP interactions: 5 interactions with chain M, 9 interactions with chain Q, 11 interactions with chain F, 8 interactions with chain G Hydrogen bonds: M:Q.329, M:K.338, M:K.338, M:Y.339, Q:V.55, F:N.88 Salt bridges: M:K.338, F:R.91, F:R.135 Hydrophobic interactions: Q:Y.41, Q:Y.41, Q:L.45, Q:L.45, Q:I.46, Q:L.56, Q:L.56, F:W.16, F:L.94, F:L.101, F:V.127, F:I.131, F:I.131, F:R.135, G:I.239, G:I.242, G:I.242, G:I.242, G:L.245, G:L.249, G:L.257, G:L.257 Water bridges: Q:L.56, F:R.135 CDL.17: 38 residues within 4Å: Chain E: T.576, I.577, S.579, Q.580, T.594, S.598, L.601, L.602, F.604 Chain G: M.100, P.110, F.113, L.153, T.156, L.157, L.160 Chain H: A.2, L.6, Y.9, A.25, I.28, G.29, 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.16, CDL.18 34 PLIP interactions: 6 interactions with chain G, 7 interactions with chain E, 21 interactions with chain H Hydrophobic interactions: G:P.110, G:F.113, G:L.153, G:T.156, G:L.157, G:L.160, E:I.577, E:T.594, E:L.601, E:L.602, E:F.604, H:L.6, H:Y.9, H:A.25, H:I.28, H:A.31, H:V.35, H:V.35, H:V.36, H:V.36, H:Y.39, H:Y.39, H:Y.39, H:A.63, H:I.66, H:F.70, H:F.70, H:F.70, H:V.125 Hydrogen bonds: E:S.579, E:Q.580, H:Y.59 Salt bridges: H:K.44, H:K.44 CDL.18: 21 residues within 4Å: Chain E: T.560, I.561, L.562, T.565, L.568, A.569, K.572 Chain H: L.101, G.109, I.110, A.113, A.114, A.116, Y.117, T.121 Ligands: 3PE.6, 3PE.11, PC1.12, 3PE.16, CDL.17, 3PE.26 14 PLIP interactions: 7 interactions with chain H, 7 interactions with chain E Hydrophobic interactions: H:L.101, H:I.110, H:A.113, H:A.113, H:A.114, H:A.116, H:Y.117, E:T.560, E:I.561, E:L.562, E:T.565, E:A.569 Salt bridges: E:K.572, E:K.572 CDL.19: 36 residues within 4Å: Chain E: L.9, L.12, I.13, T.16, A.20, N.65, L.78, F.80, I.130 Chain I: L.76, G.79, I.80, V.82, V.83, I.86, T.87, N.90, V.91, E.95, H.115 Chain L: P.43, V.47, R.48, I.51, H.55 Chain T: W.80, Y.84, Y.85, H.89 Chain Y: V.100, T.104, A.107, Y.108 Ligands: PC1.8, CDL.9, PC1.28 36 PLIP interactions: 8 interactions with chain E, 11 interactions with chain I, 9 interactions with chain T, 3 interactions with chain Y, 5 interactions with chain L Hydrophobic interactions: E:L.9, E:L.12, E:I.13, E:I.13, E:T.16, E:A.20, E:L.78, E:I.130, I:L.76, I:I.80, I:V.82, I:V.83, I:V.83, I:I.86, I:I.86, T:W.80, T:W.80, T:W.80, T:W.80, T:Y.84, T:Y.84, T:Y.85, T:Y.85, Y:V.100, Y:Y.108, L:V.47, L:V.47, L:I.51 Hydrogen bonds: I:N.90, I:N.90, I:E.95, Y:Y.108, L:H.55 Salt bridges: I:H.115, T:H.89, L:R.48 CDL.21: 31 residues within 4Å: Chain 0: F.23, L.27, N.31, K.34 Chain F: L.2, I.5, M.9, M.10, M.12, P.13, S.53, T.55, F.56, L.101, L.104, F.105, F.117, M.121 Chain G: P.256, L.337, P.338 Chain K: F.169, W.170, T.171, M.172 Chain Q: T.29, P.31, R.32, A.34, Y.35, F.38 34 PLIP interactions: 7 interactions with chain 0, 13 interactions with chain F, 3 interactions with chain G, 3 interactions with chain K, 8 interactions with chain Q Hydrophobic interactions: 0:F.23, 0:F.23, 0:L.27, F:L.2, F:I.5, F:I.5, F:M.12, F:P.13, F:F.56, F:L.101, F:L.104, F:F.105, G:P.256, G:L.337, G:P.338, K:F.169, Q:R.32, Q:A.34, Q:Y.35, Q:Y.35, Q:F.38, Q:F.38, Q:F.38, Q:F.38 Hydrogen bonds: 0:N.31, 0:N.31, 0:K.34, F:S.53, F:T.55, F:T.55, K:T.171, K:T.171 Water bridges: 0:D.28, F:L.54 CDL.25: 21 residues within 4Å: Chain G: M.323, T.324, L.325, T.328, L.332, L.336, L.339 Chain Q: D.47, R.62, L.65, Y.66, S.69, F.70, F.72, V.73, L.77 Chain Z: K.43, L.46, T.47, T.50 Ligands: 3PE.24 29 PLIP interactions: 19 interactions with chain Q, 8 interactions with chain G, 2 interactions with chain Z Hydrophobic interactions: Q:R.62, Q:L.65, Q:Y.66, Q:Y.66, Q:Y.66, Q:F.70, Q:F.70, Q:F.72, Q:F.72, Q:V.73, Q:V.73, Q:L.77, G:L.325, G:L.325, G:L.332, G:L.336, G:L.339, Z:L.46 Hydrogen bonds: Q:Y.66, G:M.323, G:L.325 Water bridges: Q:R.51, Q:R.51, Q:R.53, Q:R.53, Q:R.62, G:R.322 Salt bridges: Q:R.62, Z:K.43

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

ZMP.20: 17 residues within 4Å: Chain J: D.112, S.113, L.114 Chain V: H.12, Q.13, V.16, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67, E.70, F.71 8 PLIP interactions: 2 interactions with chain J, 6 interactions with chain V Hydrophobic interactions: J:L.114, V:Q.13, V:V.16, V:A.60, V:A.67, V:E.70 Hydrogen bonds: J:S.113, V:Q.13

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.22: 13 residues within 4Å: Chain M: I.66, S.71, E.88, L.114, F.117, Y.118, Q.132, L.135, R.139, R.161, F.169, M.173, Y.233 5 PLIP interactions: 5 interactions with chain M Hydrogen bonds: M:Q.132, M:Y.233 Salt bridges: M:K.70, M:R.161 pi-Stacking: M:F.169

1 x MYR: MYRISTIC ACID(Covalent)

MYR.27: 7 residues within 4Å: Chain E: L.413, Y.485, T.489 Chain U: G.2, A.3, L.5 Chain X: T.152 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain U Hydrophobic interactions: E:L.413, E:T.489, U: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

NADH-ubiquinone oxidoreductase chain 3: A
NADH-ubiquinone oxidoreductase chain 1: B
NADH-ubiquinone oxidoreductase chain 6: C
NADH-ubiquinone oxidoreductase chain 4L: D
NADH-ubiquinone oxidoreductase chain 5: E
NADH-ubiquinone oxidoreductase chain 4: F
NADH-ubiquinone oxidoreductase chain 2: G
Mitochondrial complex I, B14.7 subunit: H
NADH:ubiquinone oxidoreductase subunit B5: I
Acyl carrier protein: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: K
Mitochondrial complex I, PDSW subunit: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: M
NADH:ubiquinone oxidoreductase subunit S5: N
NADH:ubiquinone oxidoreductase subunit A3: O
NADH:ubiquinone oxidoreductase subunit B3: P
NADH dehydrogenase [ubiquinone] 1 subunit C2: Q
NADH:ubiquinone oxidoreductase subunit B4: R
Mitochondrial complex I, B16.6 subunit: S
Mitochondrial complex I, B17 subunit: T
NADH:ubiquinone oxidoreductase subunit B7: U
NADH:ubiquinone oxidoreductase subunit B9: V
NADH:ubiquinone oxidoreductase subunit B2: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: X
Mitochondrial complex I, ESSS subunit: Y
Mitochondrial complex I, KFYI subunit: Z
Mitochondrial complex I, MNLL subunit: 0
Mitochondrial complex I, MWFE subunit: 1
Mitochondrial complex I, ND4L subunit: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
J

D
K

E
L

F
M

G
N

H
V

I
W

J
X

K
Y

L
Z

M
k

N
l

O
m

P
n

Q
o

R
p

S
q

T
r

U
s

V
t

W
u

X
v

Y
w

Z
x

0
y

1
z

2
4

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

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

Mitochondrial complex I, ND4L subunit

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