SMTL ID : 7vbn.1

Matrix arm of deactive state CI from DQ-NADH dataset

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-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-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 SF4.4: 14 residues within 4Å: Chain B: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, P.127, 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 SF4.5: 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 SF4.6: 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: 4 interactions with chain C, 1 interactions with chain P, Metal complexes: C:C.31, C:C.32, C:C.96, C:C.126, P:H.145 SF4.11: 12 residues within 4Å: Chain L: H.96, P.97, D.99, C.100, C.103, Q.105, G.106, 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 SF4.12: 13 residues within 4Å: Chain L: M.145, C.148, I.149, Q.150, C.151, T.152, R.153, C.154, V.178, 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: 20 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 Ligands: NAI.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.177, A:I.178, A:E.181, A:E.181, A:A.399, A:L.400 Hydrogen bonds: A:R.61, A:G.62, A:N.89, A:D.91, A:E.92, A:G.93, A:E.182, A:N.217, A:N.217, A:T.220 Water bridges: A:G.63, A:G.65, A:N.89, A:N.89, A:G.180, A:G.180 Salt bridges: A:K.71

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 14 residues within 4Å: Chain A: G.62, G.63, A.64, F.66, K.71, E.92, G.93, E.94, Y.177, E.182, F.202, G.323, A.399 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.94, A:Y.177 Hydrogen bonds: A:G.62, A:K.71, A:G.93, A:E.94, A:E.182, A:N.217 Water bridges: A:F.66 Salt bridges: A:K.199, A:K.199 pi-Stacking: A:F.66, A:F.202

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

PEE.7: 9 residues within 4Å: Chain C: L.10, V.14, R.149, L.150, W.153, R.156 Chain I: D.55, F.275 Ligands: PLX.8 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:L.10, C:V.14, C:W.153, C:W.153, I:F.275 Water bridges: C:R.156 Salt bridges: C:R.156 Hydrogen bonds: I:D.55

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.8: 12 residues within 4Å: Chain C: L.10, D.12, L.13, W.16, R.19, K.145 Chain M: F.27, R.28, N.30, W.74, V.76 Ligands: PEE.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.10, C:D.12, C:L.13, C:W.16, C:W.16, C:W.16, 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)

8Q1.9: 21 residues within 4Å: Chain D: M.12, K.16, V.19, L.22, W.26, G.46, K.49, V.50, M.53, F.54, M.55, N.57, A.58, V.60, V.66, L.69, V.70, F.93 Chain F: D.43, S.44, L.45 12 PLIP interactions: 2 interactions with chain F, 10 interactions with chain D Hydrogen bonds: F:S.44, F:L.45, D:K.16, D:A.58 Hydrophobic interactions: D:W.26, D:K.49, D:F.54, D:F.54, D:V.66, D:F.93, D:F.93 Salt bridges: D:K.16

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

NDP.10: 25 residues within 4Å: Chain C: R.156 Chain I: G.25, T.27, G.28, F.29, L.30, R.50, C.51, W.73, L.94, V.95, G.96, R.97, F.104, V.109, F.110, I.132, S.133, H.134, Y.145, K.149, P.168, D.170, I.171, R.177 24 PLIP interactions: 21 interactions with chain I, 3 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:C.51, I:L.94, I:G.96, I:K.149, I:I.171, I:I.171, I:R.177 Salt bridges: I:R.50, I:R.97, I:R.97, I:R.177, C:R.156 pi-Cation interactions: I:R.50, I:R.50 Water bridges: C:R.156, C:R.156

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

FES.13: 9 residues within 4Å: Chain L: R.34, 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.16: 10 residues within 4Å: Chain N: C.103, T.105, P.107, C.108, C.144, L.145, G.146, A.147, C.148, M.153 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.14: 5 residues within 4Å: Chain L: Q.105, I.195, C.198, V.200, L.203 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:I.195, L:C.198, L:V.200, L:L.203

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 10 residues within 4Å: Chain H: S.2, A.3, T.4, I.7, L.10 Chain M: L.2, V.5, R.8, G.9, Y.22 7 PLIP interactions: 4 interactions with chain M, 3 interactions with chain H Hydrophobic interactions: M:L.2, H:I.7, H:L.10 Hydrogen bonds: M:R.8, M:Q.12, H:T.4 Salt bridges: M:R.8

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 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

2022-04-06

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, mitochondrial: 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, mitochondrial

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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