SMTL ID : 7dh0.1

Activity optimized complex I (open form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)(Covalent)

3PE.1: 7 residues within 4Å: Chain A: P.238, I.239 Chain C: P.13, W.16, T.90 Chain d: L.43, P.52 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.239, C:P.13, C:W.16 Hydrogen bonds: A:P.238 3PE.3: 13 residues within 4Å: Chain A: N.274, I.276, I.277, I.284 Chain C: V.162, Y.166, S.191, F.194, M.195, L.197, A.198 Chain Z: G.131, W.132 13 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A, 3 interactions with chain Z Hydrophobic interactions: C:V.162, C:F.194, C:F.194, C:F.194, C:M.195, C:L.197, A:I.277, A:I.284, Z:W.132, Z:W.132 Hydrogen bonds: C:Y.166, C:S.191, Z:W.132 3PE.10: 18 residues within 4Å: Chain 1: I.39 Chain I: R.233, I.234 Chain L: T.24, L.25, W.27, L.30 Chain S: I.24 Chain e: P.180, A.182, M.183, M.184, F.186, I.187, Y.277, F.280, F.293, L.296 18 PLIP interactions: 5 interactions with chain L, 1 interactions with chain S, 3 interactions with chain I, 9 interactions with chain e Hydrophobic interactions: L:L.25, L:W.27, L:W.27, L:W.27, L:L.30, S:I.24, I:I.234, e:P.180, e:P.180, e:F.186, e:F.186, e:I.187, e:Y.277, e:F.280, e:F.293, e:L.296 Salt bridges: I:R.233, I:R.233

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 15 residues within 4Å: Chain 7: G.33, A.37, I.38 Chain C: L.446, L.447, L.449, N.450 Chain b: S.74, V.77, A.78 Chain f: M.20, S.23, N.25, W.66, H.67 9 PLIP interactions: 1 interactions with chain f, 4 interactions with chain C, 3 interactions with chain 7, 1 interactions with chain b Hydrophobic interactions: f:N.25, C:L.446, C:L.446, C:L.447, C:N.450, 7:A.37, 7:I.38, 7:I.38, b:A.78

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 12 residues within 4Å: Chain F: G.67, G.69, K.78, N.96, D.98, E.99, G.100, C.186, G.187, A.223, N.224, A.406 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:A.406 Hydrogen bonds: F:G.69, F:N.96, F:D.98, F:G.100, F:E.101, F:G.187, F:A.223, F:N.224 Salt bridges: F:K.78

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

SF4.5: 9 residues within 4Å: Chain F: Y.184, C.359, G.360, Q.361, C.362, C.365, T.403, I.404, C.405 0 PLIP interactions: SF4.7: 11 residues within 4Å: Chain H: H.101, D.104, C.105, C.108, C.114, L.116, Q.117, R.152, V.205, G.206 Chain I: M.342 3 PLIP interactions: 3 interactions with chain H, Salt bridges: H:D.104 Metal complexes: H:H.101, H:C.114 SF4.8: 10 residues within 4Å: Chain H: C.153, Q.155, C.156, T.157, R.158, C.159, V.183, C.203, P.204, L.208 0 PLIP interactions: SF4.11: 9 residues within 4Å: Chain I: R.105 Chain K: A.53, C.54, C.55, G.90, T.91, C.119, C.149, P.150 0 PLIP interactions: SF4.12: 12 residues within 4Å: Chain L: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 2 PLIP interactions: 2 interactions with chain L, Salt bridges: L:E.133 Metal complexes: L:C.87 SF4.13: 12 residues within 4Å: Chain L: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, A.130, I.131 1 PLIP interactions: 1 interactions with chain L, Metal complexes: L:C.83

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

FES.6: 9 residues within 4Å: Chain G: C.103, T.105, C.108, C.144, L.145, G.146, A.147, C.148, M.153 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.103, G:T.105, G:G.146 FES.9: 10 residues within 4Å: Chain H: P.38, F.40, C.41, Y.42, G.50, C.52, R.53, M.54, C.55, C.69 0 PLIP interactions:

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain P: C.59, G.61, H.68, C.87 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:H.68, P:C.87

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.15: 21 residues within 4Å: Chain K: R.178 Chain X: G.25, T.27, G.28, F.29, L.30, G.31, R.50, E.52, W.73, L.94, V.95, G.96, R.97, F.104, I.132, Y.145, P.168, A.169, E.170, I.171 16 PLIP interactions: 14 interactions with chain X, 2 interactions with chain K Hydrogen bonds: X:T.27, X:T.27, X:T.27, X:G.28, X:F.29, X:L.30, X:G.31, X:R.50, X:L.94, X:G.96, X:G.96, X:Y.145, X:A.169, X:I.171 Salt bridges: K:R.178 pi-Cation interactions: K:R.178

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

PC1.16: 3 residues within 4Å: Chain B: A.103, T.107 Chain Y: M.261 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.103 PC1.17: 11 residues within 4Å: Chain A: M.21, L.136, L.343, S.344 Chain O: F.2, F.3, V.5 Chain d: F.11, Q.12, F.13, R.78 9 PLIP interactions: 5 interactions with chain d, 3 interactions with chain O, 1 interactions with chain A Hydrophobic interactions: d:F.11, d:F.13, O:F.3, O:F.3, O:V.5, A:L.136 Hydrogen bonds: d:F.11, d:Q.12, d:R.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeon, T.J. et al., A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex. Antioxid.Redox Signal. (2022)

Release Date

2022-05-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
7

F
8

G
9

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
N

U
O

V
P

W
Q

X
R

Y
S

Z
T

0
U

1
V

2
W

i
M

3
X

4
Y

5
Z

6
a

7
b

8
c

9
d

a
f

b
h

c
i

d
j

e
1

f
6

g
g

h
e

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

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

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

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

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

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

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