SMTL ID : 7ak5.1

Cryo-EM structure of respiratory complex I in the deactive state from Mus musculus at 3.2 A

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain B: A.98, C.99, C.100, G.135, S.163, C.164, G.193, C.194, P.195 Chain D: R.118, R.138, H.223 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.99, B:C.100, B:C.164, B:C.194 SF4.5: 11 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, C.425, L.427 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.6: 12 residues within 4Å: Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.7: 10 residues within 4Å: Chain G: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, C.226, V.228 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.12: 11 residues within 4Å: Chain I: H.101, C.123, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:C.123, I:C.152, I:C.155, I:C.158 SF4.13: 10 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, C.119, Y.145, C.162, V.164, I.167 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.113, I:C.116, I:C.119, I:C.162

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

PC1.2: 16 residues within 4Å: Chain B: V.74, K.77, L.78, D.80, L.81, W.84, R.87, K.213 Chain H: I.39, L.46, F.49, M.53 Chain g: F.28, R.29, N.31, W.75 14 PLIP interactions: 2 interactions with chain H, 12 interactions with chain B Hydrophobic interactions: H:L.46, H:F.49, B:V.74, B:K.77, B:L.78, B:D.80, B:L.81, B:W.84, B:W.84, B:W.84 Salt bridges: B:R.87, B:R.87, B:K.213, B:K.213 PC1.10: 15 residues within 4Å: Chain H: L.175, M.183, W.272 Chain I: D.55, R.59, M.62, T.64, I.67, R.68 Chain Z: R.28, G.29, L.30, M.35 Ligands: 3PE.11 Chain h: W.13 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain Z, 1 interactions with chain h, 1 interactions with chain I Hydrophobic interactions: H:L.175, h:W.13 Hydrogen bonds: Z:R.28 Salt bridges: Z:R.28, I:R.68

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 9 residues within 4Å: Chain E: C.134, T.136, P.138, C.139, C.175, L.176, G.177, A.178, C.179 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.134, E:C.139, E:C.175, E:C.179 FES.8: 9 residues within 4Å: Chain G: C.64, Y.65, A.72, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 17 residues within 4Å: Chain F: G.87, R.88, G.89, G.90, K.98, N.116, D.118, E.119, Y.204, G.207, E.209, V.242, A.243, N.244, T.247, A.426, L.427 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:Y.204, F:Y.204, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:K.98, F:N.116, F:E.119, F:G.207, F:E.209, F:N.244, F:T.247 Salt bridges: F:K.98

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

3PE.9: 20 residues within 4Å: Chain 0: A.39 Chain A: M.1, L.3, Y.4, I.7, I.11 Chain H: T.76, L.77, T.80, L.81, L.98, N.99, F.104 Chain J: V.34, F.37, L.44, S.49, F.56 Chain Z: F.140, T.141 13 PLIP interactions: 5 interactions with chain J, 1 interactions with chain 0, 5 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: J:V.34, J:F.37, J:F.37, J:F.56, H:T.76, H:L.81, H:F.104, A:Y.4, A:I.7 Hydrogen bonds: J:S.49, 0:A.39, H:N.99, H:N.99 3PE.11: 19 residues within 4Å: Chain 1: V.20, V.24 Chain D: R.266 Chain H: P.180, M.183, F.186, I.187, I.273, Y.277, L.288, N.292, F.293, L.296 Chain I: R.59, I.60, L.61, W.63 Chain Z: L.43 Ligands: PC1.10 15 PLIP interactions: 9 interactions with chain H, 2 interactions with chain 1, 1 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: H:P.180, H:F.186, H:F.186, H:F.186, H:F.186, H:I.187, H:Y.277, H:F.293, H:L.296, 1:V.20, 1:V.24, I:L.61, I:W.63 Salt bridges: D:R.266 Hydrogen bonds: I:R.59 3PE.14: 12 residues within 4Å: Chain L: Q.170, L.173, Y.174, F.227, G.228, I.533, H.534, T.537, S.541 Chain M: M.405 Chain b: N.115, R.116 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:L.173, L:F.227, L:I.533, L:T.537 Hydrogen bonds: L:Q.170 Salt bridges: L:H.534, L:H.534 3PE.16: 15 residues within 4Å: Chain L: T.566 Chain M: I.155, L.166, S.191, N.192, L.194, L.195, L.197 Chain N: N.274, L.276, I.277, T.280, L.281 Chain Y: L.126, W.135 11 PLIP interactions: 4 interactions with chain N, 3 interactions with chain M, 3 interactions with chain Y, 1 interactions with chain L Hydrophobic interactions: N:L.276, N:I.277, N:T.280, N:L.281, M:I.155, M:L.197, Y:L.126, Y:W.135, Y:W.135, L:T.566 Hydrogen bonds: M:S.191 3PE.17: 19 residues within 4Å: Chain 6: L.97, T.101, A.105 Chain L: W.66, H.67 Chain M: I.67, L.68, W.71, P.371, I.445, L.446, L.447, T.448, T.449, S.450, K.452 Ligands: CDL.15, CDL.26, 3PE.27 10 PLIP interactions: 9 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: M:I.67, M:W.71, M:P.371, M:L.446, M:L.447, M:T.448, 6:L.97 Hydrogen bonds: M:T.449, M:S.450 Salt bridges: M:K.452 3PE.18: 17 residues within 4Å: Chain 3: M.47 Chain M: W.16, V.90, L.94, S.97, M.98, L.105, I.127, I.131, R.135 Chain N: P.238, A.239, T.242, S.301, M.304 Chain O: N.329 Ligands: CDL.24 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: M:W.16, M:W.16, M:V.90, M:L.105, M:I.127, M:I.127, M:I.131 Hydrogen bonds: M:R.135, O:N.329 3PE.25: 7 residues within 4Å: Chain 5: F.20, R.28 Chain 6: F.99 Chain 7: F.125, Y.126 Chain M: L.36, T.40 3 PLIP interactions: 1 interactions with chain 6, 2 interactions with chain 5 Hydrophobic interactions: 6:F.99, 5:F.20 Salt bridges: 5:R.28 3PE.27: 11 residues within 4Å: Chain 8: F.80, Y.84, H.88, K.92 Chain L: F.12, I.13, T.65, W.66, M.78 Ligands: 3PE.17, CDL.26 9 PLIP interactions: 6 interactions with chain 8, 3 interactions with chain L Hydrophobic interactions: 8:F.80, 8:Y.84, 8:Y.84, 8:Y.84, L:F.12, L:F.12, L:T.65 Salt bridges: 8:H.88, 8:K.92

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 26 residues within 4Å: Chain 6: L.97, T.101 Chain 7: L.68, M.71, K.72 Chain L: L.16, I.19, S.22, M.23, M.78, R.116, K.119, Y.120, L.123, Q.139, I.142, M.150 Chain M: P.353, T.357, W.358, L.364, L.369, P.371, I.445 Ligands: 3PE.17, CDL.26 18 PLIP interactions: 11 interactions with chain L, 6 interactions with chain M, 1 interactions with chain 7 Hydrophobic interactions: L:L.16, L:I.19, L:L.123, L:Q.139, L:I.142, L:I.142, M:W.358, M:L.364, M:L.369, M:P.371, M:I.445 Hydrogen bonds: L:R.116, L:Y.120, M:P.353 Salt bridges: L:K.119, L:K.119, L:K.119, 7:K.72 CDL.24: 23 residues within 4Å: Chain 3: K.25, N.27, P.29, R.30, V.32, Y.33 Chain 5: F.22, L.26, K.29, D.30, K.33 Chain M: L.2, L.9, M.55, M.108, M.117 Chain N: P.338, L.339 Chain X: F.169, W.170, T.171, V.172 Ligands: 3PE.18 10 PLIP interactions: 3 interactions with chain 5, 2 interactions with chain M, 3 interactions with chain X, 1 interactions with chain 3, 1 interactions with chain N Hydrophobic interactions: 5:F.22, M:L.2, M:L.9, X:F.169, N:P.338 Salt bridges: 5:K.29, 5:K.33, 3:K.25 Hydrogen bonds: X:T.171, X:T.171 CDL.26: 24 residues within 4Å: Chain 6: T.101, T.102, A.105, Y.106 Chain 7: I.83, T.87, N.90, I.91, E.95, H.115 Chain 8: W.79, F.80, Y.83, H.88 Chain L: W.66, W.68, K.77, N.136, F.138 Chain M: T.449 Ligands: CDL.15, 3PE.17, 3PE.27 Chain f: R.49 19 PLIP interactions: 7 interactions with chain 7, 6 interactions with chain 8, 2 interactions with chain L, 1 interactions with chain f, 3 interactions with chain 6 Hydrophobic interactions: 7:I.83, 7:T.87, 7:N.90, 8:W.79, 8:W.79, 8:F.80, 8:Y.83, 8:Y.83, L:W.66, L:F.138, 6:T.101, 6:Y.106 Hydrogen bonds: 7:N.90, 7:N.90, 7:E.95, 6:Y.106 Salt bridges: 7:H.115, 8:H.88, f:R.49 CDL.28: 19 residues within 4Å: Chain 0: M.1, W.2, F.3, L.6, P.7 Chain H: P.42, Y.43 Chain I: F.78 Chain g: L.3, V.6, R.9, G.10, Q.13, I.33 Chain h: S.2, A.3, T.4, I.7, L.10 12 PLIP interactions: 2 interactions with chain H, 4 interactions with chain g, 3 interactions with chain h, 2 interactions with chain 0, 1 interactions with chain I Hydrophobic interactions: H:P.42, H:Y.43, g:V.6, g:I.33, h:L.10, 0:F.3, 0:L.6, I:F.78 Hydrogen bonds: g:R.9, h:T.4, h:T.4 Salt bridges: g:R.9

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.19: 18 residues within 4Å: Chain O: I.66, C.67, S.68, G.69, K.70, N.71, E.88, L.114, Y.118, Q.132, L.135, R.139, E.160, R.161, D.166, F.169, E.226, Y.233 17 PLIP interactions: 17 interactions with chain O Hydrogen bonds: O:S.68, O:S.68, O:K.70, O:N.71, O:Y.118, O:Q.132, O:Q.132, O:R.139, O:E.160, O:R.161, O:R.161, O:E.226 Salt bridges: O:K.70, O:K.70, O:K.221 pi-Stacking: O:F.169, O:F.169

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.20: 23 residues within 4Å: Chain B: R.224 Chain P: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, I.130, G.131, R.132, F.139, V.167, S.168, H.169, K.184, P.203, S.204, D.205, I.206, R.212 20 PLIP interactions: 19 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:P.203, P:I.206 Hydrogen bonds: P:T.62, P:T.62, P:F.64, P:L.65, P:C.86, P:L.129, P:I.130, P:G.131, P:R.132, P:K.184, P:I.206 Salt bridges: P:R.85, P:R.132, P:R.212, P:R.212, B:R.224 pi-Stacking: P:F.139 pi-Cation interactions: P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.21: 4 residues within 4Å: Chain R: C.79, H.88, C.104, C.107 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.79, R:H.88, R:C.104, R:C.107

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)

EHZ.22: 15 residues within 4Å: Chain T: D.111, S.112 Chain W: K.32, V.35, W.42, T.49, K.65, M.69, M.71, N.73, A.74, V.76, V.82, L.85, F.109 10 PLIP interactions: 9 interactions with chain W, 1 interactions with chain T Hydrophobic interactions: W:K.32, W:W.42, W:W.42, W:K.65, W:F.109, W:F.109 Hydrogen bonds: W:M.69, W:N.73, T:S.112 Salt bridges: W:K.32 EHZ.23: 18 residues within 4Å: Chain U: M.105, D.111, S.112, L.113 Chain d: Q.13, A.23, L.27, M.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67, E.70, F.71 15 PLIP interactions: 14 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:A.23, d:L.27, d:F.48, d:F.48, d:A.67, d:E.70, d:F.71 Hydrogen bonds: d:Q.13, d:R.47, d:K.52, d:K.52, d:K.52, U:S.112 Salt bridges: d:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Structural basis for a complex I mutation that blocks pathological ROS production. Nat Commun (2021)

Release Date

2021-02-03

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: I
NADH-ubiquinone oxidoreductase chain 6: J
NADH-ubiquinone oxidoreductase chain 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: S
Acyl carrier protein, mitochondrial: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: X
MCG5603: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: 1
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C2: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
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

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

Membrane

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MCG5603

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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