SMTL ID : 7dgz.1

Activity optimized complex I (closed 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

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

3PE.1: 5 residues within 4Å: Chain A: P.238, I.239 Chain C: W.16, T.90 Chain d: L.43 4 PLIP interactions: 1 interactions with chain d, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: d:L.43, C:W.16, A:I.239 Hydrogen bonds: C:T.90 3PE.3: 10 residues within 4Å: Chain A: I.276, I.277 Chain C: A.155, P.159, A.163, Y.166, S.191, F.194, A.198 Chain Z: W.132 7 PLIP interactions: 3 interactions with chain Z, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: Z:W.132, Z:W.132, A:I.276, A:I.277, C:A.163 Hydrogen bonds: Z:W.132, C:Y.166 3PE.10: 16 residues within 4Å: Chain I: R.233, I.234 Chain L: T.24, L.25, W.27, L.30 Chain S: L.27 Chain e: P.180, M.183, M.184, F.186, F.198, Y.277, F.280, F.293, L.296 13 PLIP interactions: 8 interactions with chain e, 1 interactions with chain S, 2 interactions with chain I, 2 interactions with chain L Hydrophobic interactions: e:P.180, e:F.186, e:F.186, e:F.198, e:Y.277, e:F.280, e:F.293, e:L.296, S:L.27, I:I.234, L:W.27, L:L.30 Salt bridges: I:R.233 3PE.20: 17 residues within 4Å: Chain 1: F.139, W.141, Y.142 Chain B: L.7, F.11 Chain E: G.38, V.39, L.45, S.50, L.54, F.57 Chain Q: A.39, H.40 Chain e: I.76, M.98, N.99, F.104 13 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B, 5 interactions with chain e, 1 interactions with chain Q, 2 interactions with chain 1 Hydrophobic interactions: E:L.45, E:L.54, E:F.57, B:F.11, e:I.76, e:F.104, 1:W.141, 1:W.141 Hydrogen bonds: E:S.50, e:N.99, e:N.99, e:L.100, Q:A.39

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 14 residues within 4Å: Chain 7: L.30, A.37, I.38, T.41 Chain C: L.446, L.447, L.449, N.450 Chain b: V.77, A.78 Chain f: M.20, S.23, N.25, W.66 14 PLIP interactions: 5 interactions with chain C, 2 interactions with chain b, 1 interactions with chain f, 6 interactions with chain 7 Hydrophobic interactions: C:L.446, C:L.446, C:L.446, C:L.449, b:V.77, b:A.78, f:N.25, 7:L.30, 7:A.37, 7:I.38, 7:I.38, 7:T.41, 7:T.41 Hydrogen bonds: C:N.450 CDL.15: 10 residues within 4Å: Chain 0: E.2, V.6, L.7, Q.13 Chain Q: W.2, F.3 Chain V: R.5, F.6, I.7, W.9 6 PLIP interactions: 5 interactions with chain V, 1 interactions with chain Q Hydrophobic interactions: V:F.6, V:W.9, Q:F.3 Hydrogen bonds: V:R.5, V:F.6 Salt bridges: V:R.5

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 16 residues within 4Å: Chain F: G.69, K.78, N.96, D.98, E.99, G.100, E.101, C.186, G.187, E.188, E.189, V.222, A.223, N.224, S.302, A.406 11 PLIP interactions: 11 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:C.186, F:G.187, F:E.189, F:N.224 Salt bridges: F:K.78

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

SF4.5: 11 residues within 4Å: Chain F: Y.184, P.203, C.359, G.360, C.362, C.365, T.403, I.404, C.405, L.407, G.408 1 PLIP interactions: 1 interactions with chain F, Metal complexes: F:Y.184 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 1 PLIP interactions: 1 interactions with chain H, Metal complexes: H:H.101 SF4.8: 13 residues within 4Å: Chain H: M.150, C.153, Q.155, C.156, T.157, R.158, C.159, V.183, C.203, P.204, V.205, A.207, L.208 0 PLIP interactions: SF4.11: 9 residues within 4Å: Chain I: R.105, H.190 Chain K: A.53, C.54, C.55, T.91, C.119, C.149, P.150 0 PLIP interactions: SF4.12: 11 residues within 4Å: Chain L: C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 3 PLIP interactions: 3 interactions with chain L, Salt bridges: L:E.133 Metal complexes: L:C.87, L:C.116 SF4.13: 11 residues within 4Å: Chain L: C.77, I.78, A.79, C.80, K.81, L.82, C.83, C.126, V.128, 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: 8 residues within 4Å: Chain G: C.103, T.105, C.108, C.144, L.145, G.146, A.147, C.148 1 PLIP interactions: 1 interactions with chain G, Metal complexes: G:T.105 FES.9: 9 residues within 4Å: Chain H: F.40, C.41, A.49, G.50, N.51, C.52, M.54, C.55, C.69 0 PLIP interactions:

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain P: C.59, G.61, H.68, C.84, C.87 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:H.68, P:C.87

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

PC1.16: 12 residues within 4Å: Chain B: A.99, W.106 Chain S: F.7, V.11, E.15, V.17, L.18, F.22, G.26 Chain e: K.291, N.292, P.295 8 PLIP interactions: 2 interactions with chain B, 1 interactions with chain e, 5 interactions with chain S Hydrophobic interactions: B:A.99, B:W.106, e:P.295, S:L.18, S:L.18, S:F.22, S:F.22, S:F.22 PC1.17: 11 residues within 4Å: Chain A: P.256, L.257, M.335 Chain C: F.105 Chain W: F.168, W.169, T.170, M.171 Chain d: P.29, R.30, F.33 8 PLIP interactions: 1 interactions with chain C, 4 interactions with chain W, 1 interactions with chain d, 2 interactions with chain A Hydrophobic interactions: C:F.105, W:F.168, W:F.168, d:F.33, A:L.257, A:M.335 Hydrogen bonds: W:T.170, W:M.171 PC1.19: 4 residues within 4Å: Chain A: I.4, I.5 Chain B: T.107 Chain Y: M.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.4, A:I.5 PC1.21: 12 residues within 4Å: Chain A: M.21, Y.143, L.343, S.344 Chain O: P.1, F.2, F.3, V.5 Chain d: F.11, Q.12, F.13, R.78 7 PLIP interactions: 5 interactions with chain d, 2 interactions with chain O Hydrophobic interactions: d:F.13, O:F.3, O:V.5 Hydrogen bonds: d:F.11, d:Q.12, d:R.78 Salt bridges: d:R.78

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

NAP.18: 20 residues within 4Å: Chain K: R.178 Chain X: T.27, G.28, F.29, L.30, G.31, R.50, E.52, L.94, V.95, G.96, R.97, F.104, I.132, S.133, H.134, Y.145, P.168, A.169, I.171 12 PLIP interactions: 11 interactions with chain X, 1 interactions with chain K Hydrogen bonds: X:G.28, X:G.28, X:L.30, X:G.31, X:R.50, X:E.52, X:L.94, X:G.96, X:G.96, X:H.134, X:Y.145 Salt bridges: K:R.178

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

Related Entries With Identical Sequence