SMTL ID : 7p7k.1

Complex I from E. coli, DDM/LMNG-purified, with DQ, 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)(Covalent)

SF4.1: 13 residues within 4Å: Chain A: I.176, P.194, S.347, C.348, G.349, W.350, C.351, C.354, T.393, F.394, C.395, H.397, A.398 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.348, A:C.351, A:C.354, A:C.395 SF4.4: 13 residues within 4Å: Chain C: H.98, D.101, C.102, C.105, E.107, 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 SF4.5: 13 residues within 4Å: Chain C: C.150, I.151, A.152, C.153, Y.154, R.155, C.156, F.180, C.200, P.201, T.202, V.204, F.205 5 PLIP interactions: 5 interactions with chain C, pi-Cation interactions: C:F.180 Metal complexes: C:C.150, C:C.153, C:C.156, C:C.200 SF4.6: 11 residues within 4Å: Chain C: C.227, Q.229, C.230, I.232, G.233, C.234, L.261, C.262, R.264, G.265, R.387 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.227, C:C.230, C:C.234, C:C.262 SF4.9: 14 residues within 4Å: Chain D: R.254, R.274, H.359 Chain E: S.62, C.63, C.64, G.100, T.101, G.127, A.128, C.129, G.157, 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 SF4.10: 13 residues within 4Å: Chain F: I.17, C.39, P.40, V.41, C.43, I.44, C.68, I.69, F.70, C.71, G.72, L.73, C.74 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.39, F:C.68, F:C.71, F:C.74 SF4.11: 14 residues within 4Å: Chain F: C.29, V.30, A.31, C.32, N.33, L.34, C.35, L.46, F.61, C.78, P.79, T.80, A.82, I.83 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.29, F:C.32, F:C.35, F:C.78

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.58, R.59, G.60, A.62, K.69, N.87, D.89, E.90, M.91, Y.175, G.178, E.179, E.180, V.213, N.214, N.215, T.218, A.396, H.397 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.175, A:Y.175, A:E.179, A:A.396, A:H.397 Hydrogen bonds: A:G.60, A:N.87, A:N.87, A:E.90, A:M.91, A:G.178, A:G.178, A:E.180, A:N.214, A:N.215, A:T.218 Salt bridges: A:K.69

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

FES.3: 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 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.82, B:C.87, B:C.123, B:C.127 FES.7: 10 residues within 4Å: Chain C: Y.31, C.33, W.34, G.42, A.43, C.44, R.45, Q.46, C.47, 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.8: 4 residues within 4Å: Chain C: D.616, Q.631, E.646, D.730 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.616, C:E.646, C:D.730

4 x LFA: EICOSANE(Non-covalent)

LFA.12: 8 residues within 4Å: Chain G: I.21, V.24, V.103, W.107, P.266, F.268, I.269, T.275 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:I.21, G:V.24, G:V.103, G:V.103, G:W.107, G:W.107, G:P.266, G:F.268, G:F.268, G:I.269, G:T.275 LFA.16: 4 residues within 4Å: Chain I: Y.590, R.592, A.596 Chain M: G.95 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.590, I:A.596 LFA.22: 13 residues within 4Å: Chain J: Y.112, F.115, L.156, W.157, K.160 Chain K: F.366, W.367, A.374, V.378, L.381, M.388, Y.433, L.465 13 PLIP interactions: 8 interactions with chain K, 5 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:W.367, K:A.374, K:V.378, K:L.381, K:Y.433, K:L.465, J:Y.112, J:F.115, J:F.115, J:W.157, J:W.157 LFA.23: 6 residues within 4Å: Chain K: F.278, W.408, W.409, G.412 Ligands: 3PE.20, 3PE.21 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:F.278, K:W.409

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

3PE.13: 17 residues within 4Å: Chain G: M.88, I.89, T.92, D.111, L.112, N.113, I.114, F.118, L.125 Chain H: H.13, F.16, A.17, L.20, I.24 Chain M: F.44, Y.49 Ligands: 3PE.14 15 PLIP interactions: 6 interactions with chain H, 6 interactions with chain G, 3 interactions with chain M Hydrophobic interactions: H:F.16, H:A.17, H:L.20, H:I.24, G:I.89, G:L.112, G:I.114, G:F.118, G:L.125, M:F.44, M:F.44 Salt bridges: H:H.13, H:H.13 Hydrogen bonds: G:N.113, M:Y.49 3PE.14: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, C.8, L.37, A.38, G.41, F.44, S.45, Y.49 Ligands: 3PE.13 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain M Salt bridges: H:H.13 Hydrophobic interactions: M:F.3, M:I.7, M:L.37 Hydrogen bonds: M:M.1, M:Y.49 3PE.15: 24 residues within 4Å: Chain I: L.12, A.19, F.20, R.22, G.23, R.115, Y.119, L.122, V.129, L.141, G.145, L.148 Chain J: W.378, K.382, W.383, A.386, L.387, L.389, F.390, M.398, P.399, V.472, V.473, F.480 14 PLIP interactions: 7 interactions with chain J, 7 interactions with chain I Hydrophobic interactions: J:W.383, J:L.387, J:L.389, J:V.472, J:V.473, J:F.480, I:L.12, I:L.12, I:L.122, I:V.129, I:L.141, I:L.148 Hydrogen bonds: J:W.378, I:R.22 3PE.17: 14 residues within 4Å: Chain I: F.296, L.299, F.363, L.427, R.431, I.435, L.511, W.512, V.519, I.522, A.523, G.528, L.531, W.535 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:F.296, I:L.299, I:L.511, I:W.512, I:I.522, I:L.531, I:W.535, I:W.535, I:W.535 Salt bridges: I:R.431 3PE.18: 18 residues within 4Å: Chain I: M.569, N.570, P.572, A.573, S.576, R.577 Chain J: T.169, I.176, Y.177, A.180, S.181, I.229, V.233, L.240 Chain K: L.289, A.419, Y.423 Ligands: 3PE.20 18 PLIP interactions: 3 interactions with chain I, 11 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: I:A.573, I:R.577, J:I.176, J:I.176, J:Y.177, J:A.180, J:I.229, J:I.229, J:V.233, J:L.240, J:L.240, K:L.289, K:A.419, K:Y.423, K:Y.423 Salt bridges: I:R.577 Hydrogen bonds: J:T.169, J:T.169 3PE.19: 18 residues within 4Å: Chain I: A.165, M.168, K.169, V.172, V.173, V.176, P.234, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, A.438, H.441, R.442 19 PLIP interactions: 6 interactions with chain J, 13 interactions with chain I Hydrophobic interactions: J:F.306, J:F.427, J:F.427, J:F.427, I:M.168, I:V.172, I:V.173, I:V.176, I:V.176, I:P.234, I:Y.545, I:Y.545, I:F.549, I:F.549, I:F.549, I:V.550, I:L.554 Salt bridges: J:H.441, J:R.442 3PE.20: 12 residues within 4Å: Chain I: S.576 Chain J: S.216, S.217, Y.221, L.222, L.225, L.240, L.293 Chain K: V.416 Ligands: 3PE.18, 3PE.21, LFA.23 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:Y.221, J:L.225, J:L.240, J:L.293, K:V.416 Hydrogen bonds: J:S.216, J:S.216 3PE.21: 15 residues within 4Å: Chain J: V.184, A.191, V.195, V.219, L.222, L.223, L.225, G.226, I.229 Chain K: H.406, W.408, G.412, V.415 Ligands: 3PE.20, LFA.23 14 PLIP interactions: 8 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:A.191, J:V.219, J:L.222, J:L.222, J:L.223, J:L.225, K:W.408, K:W.408, K:W.408, K:W.408, K:V.415 Salt bridges: K:H.406

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
NADH-quinone oxidoreductase subunit H: G
NADH-quinone oxidoreductase subunit A: H
Proton-translocating NADH-quinone oxidoreductase, chain L: I
NADH dehydrogenase I subunit M: J
NADH-quinone oxidoreductase subunit N: 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
H

H
A

I
L

J
M

K
N

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

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit A

Proton-translocating NADH-quinone oxidoreductase, chain L

NADH dehydrogenase I subunit M

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit J

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