SMTL ID : 7p61.1

Complex I from E. coli, DDM-purified, with NADH, Resting state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: I.179, P.197, S.350, C.351, W.353, C.354, C.357, T.396, F.397, C.398, H.400 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.351, A:C.354, A:C.357, A:C.398 SF4.5: 12 residues within 4Å: Chain C: H.98, D.101, C.102, C.105, G.108, C.111, L.113, Q.114, R.149, T.202, G.203 Chain D: I.516 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.101 Metal complexes: C:H.98, C:C.102, C:C.105, C:C.111 SF4.6: 12 residues within 4Å: Chain C: C.150, I.151, A.152, C.153, Y.154, C.156, F.180, C.200, P.201, T.202, V.204, F.205 4 PLIP interactions: 4 interactions with chain C, pi-Cation interactions: C:F.180 Metal complexes: C:C.150, C:C.156, C:C.200 SF4.7: 11 residues within 4Å: Chain C: C.227, Q.229, C.230, I.232, G.233, C.234, C.262, R.264, G.265, A.386, R.387 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.227, C:C.230, C:C.234, C:C.262 SF4.10: 12 residues within 4Å: Chain D: R.254, R.274, H.359 Chain E: C.63, C.64, A.99, G.100, G.127, A.128, C.129, C.158, P.159 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.63, E:C.64, E:C.129, E:C.158 SF4.11: 12 residues within 4Å: Chain F: I.15, C.37, V.39, C.41, I.42, C.66, I.67, F.68, C.69, G.70, L.71, C.72 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.37, F:C.66, F:C.72 SF4.12: 12 residues within 4Å: Chain F: C.27, V.28, A.29, C.30, C.33, L.44, F.59, C.76, P.77, T.78, A.80, I.81 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.27, F:C.30, F:C.33, F:C.76

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, I.179, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399, H.400 Ligands: NAI.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.179, A:E.182, A:E.182, A:A.399, A:H.400 Hydrogen bonds: A:G.63, A:N.90, A:D.92, A:M.94, A:G.181, A:E.183, A:N.217, A:N.218, A:T.221 Salt bridges: A:K.72

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

NAI.3: 17 residues within 4Å: Chain A: G.63, G.64, A.65, F.67, K.72, L.75, E.93, E.95, Y.178, E.183, K.200, F.203, R.320, G.322, T.323, A.399 Ligands: FMN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.95 Hydrogen bonds: A:E.95, A:E.183, A:R.320 Salt bridges: A:K.200, A:K.200 pi-Stacking: A:F.67, A:F.203

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

FES.4: 10 residues within 4Å: Chain B: C.82, S.84, V.86, C.87, C.123, L.124, G.125, N.126, C.127, N.132 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.82, B:C.87, B:C.127 FES.8: 9 residues within 4Å: Chain C: Y.31, C.33, W.34, V.41, C.44, R.45, C.47, M.64, C.66 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.33, C:C.44, C:C.47, C:C.66

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain C: D.616, Q.631, E.646, D.728, D.730 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.616, C:E.646, C:D.730

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

3PE.13: 27 residues within 4Å: Chain G: L.12, F.15, A.19, F.20, R.22, G.23, S.114, R.115, Y.119, L.122, S.126, V.129, L.141, G.145, L.148 Chain H: W.378, M.381, K.382, W.383, A.386, L.389, F.390, P.399, V.472, V.476, L.477, F.480 17 PLIP interactions: 9 interactions with chain H, 8 interactions with chain G Hydrophobic interactions: H:W.383, H:L.389, H:F.390, H:F.390, H:V.472, H:V.476, H:L.477, H:F.480, G:L.12, G:F.15, G:F.20, G:L.122, G:V.129, G:L.141, G:L.148 Hydrogen bonds: H:W.378, G:R.22 3PE.14: 11 residues within 4Å: Chain G: M.168, K.169, V.172, F.549, V.550, F.553, L.554 Chain H: F.306, V.434, H.441, R.442 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:K.169, G:K.169, G:F.549, G:F.549, G:F.549, G:F.549, G:V.550, G:V.550, G:F.553, G:F.553, H:F.306, H:V.434 Hydrogen bonds: H:R.442

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.15: 10 residues within 4Å: Chain E: W.55, A.88 Chain J: R.37, L.60, D.63, M.64, M.67, F.234, F.238, V.239 10 PLIP interactions: 7 interactions with chain J, 3 interactions with chain E Hydrophobic interactions: J:L.60, J:D.63, J:M.64, J:F.234, J:F.238, J:F.238, J:V.239, E:W.55, E:W.55 pi-Stacking: E:W.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kravchuk, V. et al., A universal coupling mechanism of respiratory complex I. Nature (2022)

Release Date

2022-09-21

Peptides

NADH-quinone oxidoreductase subunit F: A
NADH dehydrogenase I subunit E: B
NADH-quinone oxidoreductase: C
NADH-quinone oxidoreductase subunit C/D: D
NADH-quinone oxidoreductase subunit B: E
NADH-quinone oxidoreductase subunit I: F
Proton-translocating NADH-quinone oxidoreductase, chain L: G
NADH dehydrogenase I subunit M: H
NADH-quinone oxidoreductase subunit N: I
NADH-quinone oxidoreductase subunit H: J
NADH-quinone oxidoreductase subunit A: K
NADH-quinone oxidoreductase subunit K: L
NADH-quinone oxidoreductase subunit J: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

C
G

D
C

E
B

F
I

G
L

H
M

I
N

J
H

K
A

L
K

M
J

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit F

NADH dehydrogenase I subunit E

NADH-quinone oxidoreductase

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

Proton-translocating NADH-quinone oxidoreductase, chain L

NADH dehydrogenase I subunit M

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit A

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit J

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