SMTL ID : 7vyh.1

Matrix arm of deactive state CI from Rotenone dataset

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-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.178, P.196, C.352, G.353, Q.354, C.355, C.358, T.396, I.397, C.398, L.400, G.401 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.352, A:C.355, A:C.358, A:C.398 SF4.3: 12 residues within 4Å: Chain B: C.77, I.78, A.79, C.80, K.81, C.83, I.94, Y.109, C.126, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.77, B:C.80, B:C.83, B:C.126 SF4.4: 12 residues within 4Å: Chain B: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.133 Metal complexes: B:C.87, B:C.116, B:C.119, B:C.122 SF4.5: 11 residues within 4Å: Chain C: A.30, C.31, C.32, G.94, S.95, C.96, C.126, P.127 Chain P: R.40, R.60, H.145 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.31, C:C.31, C:C.32, C:C.96, C:C.126 SF4.10: 11 residues within 4Å: Chain L: H.96, P.97, D.99, C.100, C.103, Q.105, C.109, L.111, Q.112, V.200, G.201 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:H.96, L:C.100, L:C.103, L:C.109 SF4.11: 11 residues within 4Å: Chain L: C.148, I.149, Q.150, C.151, T.152, R.153, C.154, C.198, V.200, A.202, L.203 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.148, L:C.151, L:C.154, L:C.198

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.60, R.61, G.62, K.71, N.89, D.91, E.92, G.93, Y.177, I.178, G.180, E.181, E.182, V.215, A.216, N.217, T.220, A.399, L.400 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.177, A:Y.177, A:I.178, A:E.181, A:A.399, A:L.400 Hydrogen bonds: A:G.62, A:N.89, A:E.92, A:G.93, A:E.182, A:V.215, A:N.217, A:N.217, A:T.220 Salt bridges: A:K.71

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.6: 7 residues within 4Å: Chain C: L.10, V.14, R.149, L.150, W.153, R.156 Ligands: PLX.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.10, C:L.150, C:L.150, C:W.153, C:W.153 Salt bridges: C:R.156

1 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.7: 11 residues within 4Å: Chain C: K.9, L.10, L.13, W.16, R.19, K.145 Chain M: F.27, R.28, N.30, W.74 Ligands: PEE.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.10, C:L.13, C:L.13, C:L.13, C:W.16 Salt bridges: C:R.19, C:R.19, C:K.145, C:K.145

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.8: 14 residues within 4Å: Chain D: K.16, W.26, M.53, M.55, N.57, A.58, V.60, V.66, L.69, G.73, F.93 Chain F: D.43, S.44, L.45 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:W.26, D:M.53, D:V.60, D:V.66, D:F.93, D:F.93, D:F.93 Hydrogen bonds: D:K.16, D:N.57, D:A.58, F:S.44, F:L.45 Salt bridges: D:K.16

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

NDP.9: 21 residues within 4Å: Chain I: G.25, T.27, G.28, F.29, L.30, R.50, W.73, L.94, V.95, G.96, R.97, F.104, V.109, F.110, I.132, H.134, Y.145, K.149, P.168, I.171, R.177 23 PLIP interactions: 22 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:P.168, I:I.171 Hydrogen bonds: I:G.25, I:T.27, I:T.27, I:T.27, I:F.29, I:L.30, I:R.50, I:C.51, I:L.94, I:G.96, I:R.97, I:K.149, I:I.171 Salt bridges: I:R.50, I:R.97, I:R.97, I:R.177, I:R.177, C:R.156 pi-Stacking: I:F.104 pi-Cation interactions: I:R.50

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

FES.12: 10 residues within 4Å: Chain L: R.34, F.35, C.36, Y.37, G.45, N.46, C.47, R.48, C.50, C.64 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.36, L:C.47, L:C.50, L:C.64 FES.15: 9 residues within 4Å: Chain N: C.103, T.105, P.107, C.108, C.144, L.145, G.146, A.147, C.148 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.103, N:C.108, N:C.144, N:C.148

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain L: Q.105, I.195, C.198, V.200, L.203 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:I.195, L:V.200, L:L.203

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 11 residues within 4Å: Chain H: S.2, A.3, T.4, V.6, I.7 Chain M: L.2, V.5, L.6, R.8, Q.12, Y.22 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain M Hydrophobic interactions: H:V.6 Hydrogen bonds: H:S.2, H:T.4, M:R.8, M:R.8 Salt bridges: M:R.8

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 5 residues within 4Å: Chain Q: C.59, G.61, H.68, C.84, C.87 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:C.59, Q:H.68, Q:C.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., The coupling mechanism of mammalian mitochondrial complex I. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-23

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: E
Acyl carrier protein: F
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: H
NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial: I
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: J
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: K
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: M
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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
T

R
W

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

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

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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