SMTL ID : 9cd6.1

Cryo-EM structure of respiratory supercomplex I in open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 18 residues within 4Å: Chain A: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.204, A:Y.204, A:E.208, A:E.208, A:A.426, A:L.427 Hydrogen bonds: A:R.88, A:G.89, A:N.116, A:E.119, A:G.120, A:E.121, A:G.207, A:E.209, A:V.242, A:N.244, A:T.247 Salt bridges: A:K.98

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

SF4.2: 14 residues within 4Å: Chain A: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, R.386, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.379, A:C.382, A:C.385, A:C.425 SF4.4: 13 residues within 4Å: Chain F: H.101, C.123, P.124, I.128, I.147, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 6 PLIP interactions: 6 interactions with chain F, Salt bridges: F:E.169 Metal complexes: F:H.101, F:C.123, F:C.152, F:C.155, F:C.158 SF4.5: 13 residues within 4Å: Chain F: C.113, I.114, A.115, C.116, K.117, L.118, C.119, I.130, Y.145, C.162, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.113, F:C.116, F:C.119, F:C.162 SF4.6: 13 residues within 4Å: Chain B: R.144, H.229 Chain G: A.70, C.71, C.72, G.107, T.108, G.134, S.135, C.136, G.165, C.166, P.167 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.71, G:C.72, G:C.136, G:C.166 SF4.9: 13 residues within 4Å: Chain B: M.381 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 5 PLIP interactions: 5 interactions with chain g, Salt bridges: g:D.127 Metal complexes: g:H.124, g:C.128, g:C.131, g:C.137 SF4.10: 12 residues within 4Å: Chain g: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, C.226, V.228, A.230 4 PLIP interactions: 4 interactions with chain g, Metal complexes: g:C.176, g:C.179, g:C.182, g:C.226

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

FES.3: 8 residues within 4Å: Chain D: C.135, T.137, P.139, C.140, C.176, A.179, C.180, M.185 2 PLIP interactions: 2 interactions with chain D, Metal complexes: D:C.135, D:C.140 FES.11: 9 residues within 4Å: Chain g: R.62, F.63, C.64, Y.65, G.73, 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 NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.7: 27 residues within 4Å: Chain G: R.196 Chain J: G.55, T.57, G.58, F.59, L.60, G.61, R.80, C.81, W.103, L.124, V.125, G.126, R.127, E.128, F.134, V.139, F.140, I.162, S.163, H.164, Y.175, K.179, P.198, D.200, I.201, R.207 20 PLIP interactions: 19 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: J:P.198, J:I.201, J:I.201 Hydrogen bonds: J:T.57, J:T.57, J:F.59, J:L.60, J:G.61, J:L.124, J:G.126, J:R.127, J:E.128, J:K.179, J:I.201, J:I.201 Salt bridges: J:R.80, J:R.127, J:R.207, G:R.196 pi-Cation interactions: J:R.80

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

ZMP.8: 17 residues within 4Å: Chain L: S.112, L.113 Chain N: M.51, K.55, V.58, W.65, K.88, V.89, M.92, F.93, N.96, A.97, V.99, V.105, L.108, G.112, F.132 13 PLIP interactions: 11 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: N:K.55, N:V.58, N:W.65, N:W.65, N:K.88, N:M.92, N:F.93, N:V.105, N:L.108 Hydrogen bonds: N:N.96, N:V.99, L:S.112, L:S.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cryo-EM structure of respiratory supercomplex I in open state. To Be Published

Release Date

2025-08-06

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: E
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: F
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: G
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1: K
Acyl carrier protein: LU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: N
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: P
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: S
NADH:ubiquinone oxidoreductase subunit A13: T
NADH:ubiquinone oxidoreductase subunit B2: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 0
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 1
NADH dehydrogenase [ubiquinone] 1 subunit C2: 2
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 3
NADH-ubiquinone oxidoreductase chain 2: 4
NADH-ubiquinone oxidoreductase chain 3: 5
NADH-ubiquinone oxidoreductase chain 4L: 6
NADH-ubiquinone oxidoreductase chain 5: 7
NADH-ubiquinone oxidoreductase chain 6: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: b
NADH-ubiquinone oxidoreductase chain 4: c
NADH-ubiquinone oxidoreductase chain 1: d
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: f
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
H

G
I

H
J

I
K

J
L

K
N

L
O

U
X

M
P

N
Q

O
R

P
S

Q
T

R
U

S
V

T
W

V
Y

W
Z

X
a

Y
c

Z
d

0
e

1
f

2
g

3
h

4
i

5
j

6
k

7
l

8
m

9
n

a
o

b
p

c
q

d
r

e
s

f
t

g
G

h
M

i
b

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

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

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

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH:ubiquinone oxidoreductase subunit A13

NADH:ubiquinone oxidoreductase subunit B2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

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-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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