SMTL ID : 7vxu.1

Matrix arm of deactive state CI from Q10 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.205, P.223, 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: 12 residues within 4Å: Chain B: C.113, I.114, A.115, C.116, K.117, C.119, I.130, Y.145, C.162, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.116, B:C.119, B:C.162 SF4.4: 12 residues within 4Å: Chain B: H.101, C.123, P.124, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.169 Metal complexes: B:C.123, B:C.152, B:C.155, B:C.158 SF4.5: 10 residues within 4Å: Chain C: A.70, C.71, C.72, S.135, C.136, C.166, P.167 Chain P: R.128, R.148, H.233 6 PLIP interactions: 1 interactions with chain P, 5 interactions with chain C, Metal complexes: P:H.233, C:C.71, C:C.71, C:C.72, C:C.136, C:C.166 SF4.10: 11 residues within 4Å: Chain L: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:H.124, L:C.128, L:C.131, L:C.137 SF4.11: 13 residues within 4Å: Chain L: 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 L, Metal complexes: L:C.176, L:C.179, L:C.182, L:C.226

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain A: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, A.426, L.427 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.204, A:Y.204, A:E.208, A:A.426, A:L.427 Hydrogen bonds: A:G.89, A:E.119, A:G.120, A:N.244 Salt bridges: A:K.98

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

PEE.6: 6 residues within 4Å: Chain C: L.50, V.54, L.190, W.193, R.196 Ligands: PLX.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.50, C:V.54, C:L.190, C:W.193 Salt bridges: C:R.58, C:R.196

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: 10 residues within 4Å: Chain C: K.49, L.53, W.56, R.59, K.185 Chain M: F.28, R.29, N.31, W.75 Ligands: PEE.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.53 Salt bridges: C:R.59, C:R.59, C:K.185, C:K.185

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

8Q1.8: 17 residues within 4Å: Chain D: K.29, V.32, W.39, V.63, M.66, F.67, M.68, N.70, A.71, V.73, V.79, L.82, G.86, F.106 Chain F: D.111, S.112, L.113 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:W.39, D:M.66, D:F.67, D:V.79, D:F.106, D:F.106 Hydrogen bonds: D:K.29, D:R.33, D:N.70, F:S.112, F:L.113 Salt bridges: D:K.29

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

NDP.9: 23 residues within 4Å: Chain C: R.196 Chain I: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, V.130, G.131, R.132, F.139, V.144, F.145, I.167, H.169, Y.180, K.184, P.203, I.206, R.212 19 PLIP interactions: 18 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:I.206 Hydrogen bonds: I:G.60, I:T.62, I:T.62, I:T.62, I:F.64, I:L.65, I:R.85, I:R.85, I:L.129, I:G.131, I:K.184, I:I.206 Salt bridges: I:R.85, I:R.132, I:R.132, I:R.212, C:R.196 pi-Cation interactions: I:R.85

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

FES.12: 9 residues within 4Å: Chain L: 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 L, Metal complexes: L:C.64, L:C.75, L:C.78, L:C.92 FES.15: 9 residues within 4Å: Chain N: C.135, T.137, P.139, C.140, C.176, L.177, G.178, A.179, C.180 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.135, N:C.140, N:C.176, N:C.180

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain L: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:I.223, L:C.226, L:V.228, L:L.231

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 8 residues within 4Å: Chain H: S.3, T.5, I.8 Chain M: L.3, V.6, R.9, G.10, Y.23 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: M:L.3 Salt bridges: M:R.9 Hydrogen bonds: H:T.5

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 5 residues within 4Å: Chain Q: C.86, G.88, H.95, C.111, C.114 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:C.86, Q:H.95, Q:C.111

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
Complex I-20kD: 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

Complex I-20kD

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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