SMTL ID : 9bwd.1

Cryo-EM structure of respiratory supercomplex I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 residues within 4Å: Chain A: G.87, R.88, G.89, K.98, N.116, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.204, A:Y.204, 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:G.207, A:E.209, A:V.242, A:N.244, A:N.244, A:T.247 Salt bridges: A:K.98

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

SF4.2: 13 residues within 4Å: Chain A: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, 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 SF4.3: 13 residues within 4Å: Chain B: M.381, I.385 Chain E: H.124, P.125, D.127, C.128, C.131, G.134, C.137, L.139, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:H.124, E:C.128, E:C.131, E:C.137 SF4.4: 13 residues within 4Å: Chain E: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, C.226, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.176, E:C.179, E:C.182, E:C.226 SF4.6: 13 residues within 4Å: Chain B: R.144, H.229 Chain F: A.132, C.133, C.134, G.169, G.196, S.197, C.198, Y.205, G.227, C.228, P.229 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.133, F:C.134, F:C.198, F:C.228 SF4.8: 13 residues within 4Å: Chain T: 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 5 PLIP interactions: 5 interactions with chain T, Salt bridges: T:E.169 Metal complexes: T:C.123, T:C.152, T:C.155, T:C.158 SF4.9: 14 residues within 4Å: Chain T: C.113, I.114, A.115, C.116, K.117, L.118, C.119, I.130, Y.145, C.162, P.163, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain T, Metal complexes: T:C.113, T:C.116, T:C.119, T:C.162

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

FES.5: 9 residues within 4Å: Chain E: R.62, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.64, E:C.75, E:C.78, E:C.92 FES.10: 9 residues within 4Å: Chain V: C.135, T.137, P.139, C.140, C.176, L.177, A.179, C.180, M.185 4 PLIP interactions: 4 interactions with chain V, Metal complexes: V:C.135, V:C.140, V:C.176, V:C.180

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

ZMP.7: 14 residues within 4Å: Chain K: S.112 Chain M: M.51, K.55, V.58, L.61, W.65, V.89, M.92, F.93, N.96, A.97, V.99, V.105, L.108 12 PLIP interactions: 10 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: M:K.55, M:W.65, M:W.65, M:V.89, M:M.92, M:N.96, M:V.105, M:L.108 Hydrogen bonds: M:N.96, K:S.112, K:S.112 Salt bridges: M:K.55

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

NDP.11: 28 residues within 4Å: Chain F: R.258 Chain W: G.55, A.56, T.57, G.58, F.59, L.60, R.80, C.81, W.103, L.124, V.125, G.126, R.127, F.134, V.139, F.140, I.143, I.162, S.163, H.164, Y.175, K.179, P.198, S.199, D.200, I.201, R.207 22 PLIP interactions: 21 interactions with chain W, 1 interactions with chain F Hydrophobic interactions: W:P.198, W:I.201, W:I.201 Hydrogen bonds: W:G.55, W:T.57, W:T.57, W:T.57, W:F.59, W:L.60, W:L.124, W:G.126, W:E.128, W:K.179, W:I.201, W:I.201 Salt bridges: W:R.80, W:R.127, W:R.127, W:R.207, F:R.258 pi-Cation interactions: W:R.80, W:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
F

E
G

F
I

G
J

H
K

I
M

J
N

K
O

Z
X

L
P

M
Q

N
U

O
V

P
Y

Q
Z

R
a

S
c

T
H

U
S

V
E

W
L

X
T

Y
W

0
b

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
l

a
m

b
n

c
o

d
p

e
q

f
r

g
s

h
t

i
R

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] iron-sulfur protein 6, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, 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 7

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] 1 alpha subcomplex subunit 10, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

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] iron-sulfur protein 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH:ubiquinone oxidoreductase subunit A13

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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] flavoprotein 3, mitochondrial

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