SMTL ID : 7z7s.1

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed 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.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400, A.401 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.351, A:C.354, A:C.357, A:C.398 SF4.5: 13 residues within 4Å: Chain C: H.99, D.102, C.103, C.106, E.108, G.109, C.112, L.114, Q.115, R.150, T.203, G.204 Chain D: I.512 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.102 Metal complexes: C:H.99, C:C.103, C:C.106, C:C.112 SF4.6: 13 residues within 4Å: Chain C: C.151, I.152, A.153, C.154, Y.155, R.156, C.157, F.181, C.201, P.202, T.203, V.205, F.206 5 PLIP interactions: 5 interactions with chain C, pi-Cation interactions: C:F.181 Metal complexes: C:C.151, C:C.154, C:C.157, C:C.201 SF4.7: 10 residues within 4Å: Chain C: C.228, Q.230, C.231, I.233, G.234, C.235, C.263, R.265, G.266, R.388 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.228, C:C.231, C:C.235, C:C.263 SF4.12: 15 residues within 4Å: Chain D: R.250, R.270, H.355 Chain E: S.62, C.63, C.64, G.100, T.101, G.127, A.128, C.129, Y.136, 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 SF4.14: 14 residues within 4Å: Chain F: I.48, C.70, P.71, V.72, C.74, I.75, C.99, I.100, F.101, C.102, G.103, L.104, C.105, L.116 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.99, F:C.102, F:C.105 SF4.15: 15 residues within 4Å: Chain F: L.50, C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, F.92, C.109, P.110, T.111, A.113, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, Y.178, I.179, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399, H.400 Ligands: NAI.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.178, A:I.179, A:E.182, A:E.182, A:A.399, A:H.400 Hydrogen bonds: A:G.63, A:N.90, A:N.90, A:D.92, A:E.93, A:M.94, A:G.181, A:G.181, A:E.183, A:N.217, A:N.218, A:N.218, A:T.221 Water bridges: A:G.64, A:G.66, A:F.67, A:G.181, A:G.181 Salt bridges: A:K.72

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

NAI.3: 18 residues within 4Å: Chain A: G.63, G.64, A.65, F.67, K.72, L.75, E.93, M.94, E.95, Y.178, E.183, K.200, F.203, R.320, G.322, T.323, A.399 Ligands: FMN.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.95, A:Y.178 Hydrogen bonds: A:K.72, A:M.94, A:E.95, A:E.183, A:R.320, A:R.320 Water bridges: A:E.93, A:E.182, A:N.218 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.92, S.94, V.96, C.97, C.133, L.134, G.135, N.136, C.137, N.142 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.92, B:C.97, B:C.133, B:C.137 FES.8: 11 residues within 4Å: Chain C: Y.32, F.33, C.34, W.35, G.43, A.44, C.45, R.46, C.48, M.65, C.67 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.45, C:C.48, C:C.67

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain C: D.617, Q.632, E.647, D.731 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.617, C:E.647, C:D.731, H2O.7, H2O.15

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

3PE.10: 27 residues within 4Å: Chain D: T.398, I.399 Chain F: M.1, E.5, G.9, F.10, Q.13 Chain G: F.196, A.200, I.201, V.204, F.212, I.248, S.249, M.252, F.278, M.281, F.282, I.285, P.292, R.293, D.295, Q.296, V.297, F.300 Chain H: R.132 Ligands: 3PE.16 22 PLIP interactions: 16 interactions with chain G, 3 interactions with chain F, 2 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: G:F.196, G:A.200, G:I.201, G:V.204, G:F.212, G:I.248, G:M.252, G:M.281, G:F.282, G:I.285, G:P.292, G:F.300, G:F.300, G:F.300, F:F.10, F:F.10, F:Q.13, D:I.399 Hydrogen bonds: G:D.295, G:Q.296, D:T.398 Salt bridges: H:R.132 3PE.16: 10 residues within 4Å: Chain F: L.6, L.7, V.8, F.10, G.11, T.12, R.15 Chain G: I.197, L.308 Ligands: 3PE.10 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.6, F:L.7, F:F.10, F:F.10, G:I.197, G:L.308 Salt bridges: F:R.15, F:R.15 3PE.18: 15 residues within 4Å: Chain G: L.96, D.111, L.112, N.113, I.114, F.118 Chain H: V.9, H.13, F.16, A.17, L.20 Chain M: F.44, Y.49, P.123 Ligands: 3PE.31 16 PLIP interactions: 7 interactions with chain G, 7 interactions with chain H, 2 interactions with chain M Hydrophobic interactions: G:L.96, G:L.112, G:I.114, G:F.118, H:F.16, H:F.16, H:A.17, H:L.20, H:L.20, M:F.44, M:F.44 Hydrogen bonds: G:N.113, G:N.113 Water bridges: G:I.114 Salt bridges: H:H.13, H:H.13 3PE.19: 29 residues within 4Å: Chain I: I.8, L.12, F.15, A.19, F.20, R.22, G.23, F.77, R.115, Y.119, L.122, S.126, V.129, L.141, G.145 Chain J: W.378, M.381, K.382, W.383, A.386, L.389, F.390, M.398, P.399, V.472, V.476, L.477, F.480 Ligands: 3PE.21 20 PLIP interactions: 8 interactions with chain I, 12 interactions with chain J Hydrophobic interactions: I:I.8, I:L.12, I:F.20, I:F.77, I:L.122, I:V.129, J:W.383, J:A.386, J:L.389, J:F.390, J:F.390, J:V.472, J:V.476, J:L.477, J:L.477, J:F.480 Water bridges: I:G.112, I:R.115 Hydrogen bonds: J:W.378, J:M.381 3PE.20: 15 residues within 4Å: Chain I: F.296, L.299, F.363, F.423, M.424, L.427, R.431, L.511, W.512, V.519, I.522, A.523, G.528, L.531, W.535 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:F.296, I:F.296, I:L.299, I:F.423, I:L.427, I:W.512, I:W.535 Salt bridges: I:R.431 3PE.21: 10 residues within 4Å: Chain I: I.8, I.9, L.12, L.64, W.65, T.66 Chain J: L.477, F.480, Y.481 Ligands: 3PE.19 13 PLIP interactions: 6 interactions with chain J, 7 interactions with chain I Hydrophobic interactions: J:L.477, J:F.480, J:F.480, J:F.480, J:Y.481, I:I.8, I:I.9, I:W.65, I:W.65, I:W.65, I:W.65 Hydrogen bonds: J:Y.481, I:T.66 3PE.22: 19 residues within 4Å: Chain I: M.569, N.570, P.572, A.573, S.576, R.577 Chain J: K.165, T.169, I.176, Y.177, A.180, S.181, I.229, V.233, L.240 Chain K: L.289, V.416, Y.423 Ligands: 3PE.26 20 PLIP interactions: 10 interactions with chain J, 6 interactions with chain K, 4 interactions with chain I Hydrophobic interactions: J:I.176, J:Y.177, 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:V.416, K:Y.423, I:P.572, I:A.573 Salt bridges: J:K.165, I:R.577, I:R.577 Hydrogen bonds: K:Y.423, K:Y.423, K:Y.423 3PE.23: 11 residues within 4Å: Chain I: F.180, F.183, M.214, W.217, M.221 Chain J: F.299, W.303, P.419, V.423, F.427, F.431 12 PLIP interactions: 8 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:F.299, J:F.299, J:W.303, J:V.423, J:F.427, J:F.427, J:F.431, J:F.431, I:F.180, I:I.187, I:W.217 Water bridges: I:N.190 3PE.24: 15 residues within 4Å: Chain I: M.168, K.169, V.172, V.173, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, A.438, H.441, R.442 13 PLIP interactions: 3 interactions with chain J, 10 interactions with chain I Hydrophobic interactions: J:F.306, J:F.427, I:K.169, I:V.172, I:V.173, I:Y.545, I:F.549, I:F.549, I:V.550, I:F.553, I:F.553, I:L.554 Salt bridges: J:R.442 3PE.25: 13 residues within 4Å: Chain J: V.184, I.187, A.188, V.195, S.216, V.219, L.222, L.223, G.226, I.229 Chain K: H.406, W.408 Ligands: 3PE.26 17 PLIP interactions: 10 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:V.184, J:I.187, J:A.188, J:V.219, J:L.222, J:L.223, J:I.229, K:W.408, K:W.408, K:W.408, K:W.408, K:W.408, K:W.408 Hydrogen bonds: J:S.216, J:S.216 Water bridges: J:N.198 Salt bridges: K:H.406 3PE.26: 9 residues within 4Å: Chain J: S.216, S.217, G.218, V.219, L.222, L.225 Ligands: 3PE.22, 3PE.25, LFA.28 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.216 3PE.29: 17 residues within 4Å: Chain K: N.46, L.49, L.52, W.53, G.56, Q.57, G.59, G.71, M.74, L.75, G.78, L.82, F.335, L.474, I.477, L.480, A.481 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:L.52, K:M.74, K:L.75, K:L.82, K:F.335, K:L.474, K:I.477, K:A.481 Hydrogen bonds: K:G.56, K:Q.57 3PE.31: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, C.8, I.11, I.34, L.37, G.41, F.44, S.45 Ligands: 3PE.18 7 PLIP interactions: 1 interactions with chain H, 6 interactions with chain M Salt bridges: H:H.13 Hydrophobic interactions: M:F.3, M:I.7, M:I.11, M:I.34 Hydrogen bonds: M:M.1, M:Y.49

2 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.11: 18 residues within 4Å: Chain D: H.220, P.221, A.223, H.224, G.225, Y.273, T.321, Q.324, V.332, F.333 Chain E: N.58, G.60, Y.65, V.66, V.69, F.72, T.73, L.86 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.65, E:V.66, E:V.69, E:V.69, E:F.72, E:T.73, E:L.86, D:V.332, D:V.332, D:F.333 DCQ.13: 10 residues within 4Å: Chain E: V.85, R.87 Chain G: S.33, R.37, M.64, M.232, F.234, F.238, Y.242, R.286 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:F.234, G:F.238, G:F.238, E:V.85 Hydrogen bonds: G:Y.242 Water bridges: G:R.286

4 x LFA: EICOSANE(Non-covalent)

LFA.17: 9 residues within 4Å: Chain G: I.21, V.24, C.28, F.98, W.107, P.266, F.268, I.269, M.279 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.21, G:V.24, G:F.98, G:W.107, G:P.266, G:F.268, G:I.269 LFA.27: 9 residues within 4Å: Chain J: Y.112, F.115, W.157 Chain K: F.366, W.367, A.374, T.377, V.378, Y.433 13 PLIP interactions: 7 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:W.367, K:A.374, K:T.377, K:V.378, K:Y.433, J:Y.112, J:Y.112, J:F.115, J:F.115, J:W.157, J:W.157 LFA.28: 6 residues within 4Å: Chain K: F.278, W.408, W.409, G.412, V.416 Ligands: 3PE.26 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:F.278, K:W.408, K:W.409, K:V.416, K:V.416 LFA.30: 5 residues within 4Å: Chain I: Y.590, R.592, A.596 Chain L: D.93 Chain M: G.95 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.590, I:A.596

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
NADH dehydrogenase subunit 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

NADH dehydrogenase subunit 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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