SMTL ID : 7p7c.1

Complex I from E. coli, DDM/LMNG-purified, Apo, Open 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: 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: 12 residues within 4Å: Chain C: H.98, D.101, C.102, C.105, E.107, G.108, C.111, L.113, Q.114, 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: 10 residues within 4Å: Chain C: C.227, Q.229, C.230, I.232, G.233, C.234, 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: 15 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, 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 SF4.10: 13 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 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.99, F:C.102, F:C.105 SF4.11: 14 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, 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: 19 residues within 4Å: Chain A: G.58, R.59, G.60, K.69, N.87, D.89, E.90, M.91, Y.175, I.176, G.178, E.179, E.180, V.213, N.214, N.215, T.218, A.396, H.397 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.175, A:Y.175, A:I.176, A:E.179, A:A.396, A:H.397 Hydrogen bonds: A:G.60, 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:N.215, A:T.218 Water bridges: A:G.63, A:G.63, A:G.63, A:N.87, A:N.87, A:G.178 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, F.32, C.33, W.34, G.42, A.43, C.44, R.45, 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 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.616, C:E.646, C:D.730, H2O.12

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

3PE.12: 22 residues within 4Å: Chain D: T.402, I.403, G.406 Chain F: M.1, E.5, L.6, G.9, F.10, Q.13, V.14, I.17 Chain G: F.196, A.200, V.204, F.212, F.278, M.281, I.285, L.289, P.292, Q.296, F.300 19 PLIP interactions: 11 interactions with chain G, 6 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: G:F.196, G:A.200, G:F.212, G:F.212, G:F.278, G:M.281, G:I.285, G:L.289, G:P.292, G:F.300, G:F.300, F:L.6, F:F.10, F:F.10, F:Q.13, F:V.14, F:I.17 Hydrogen bonds: D:T.402, D:G.406 3PE.15: 17 residues within 4Å: Chain G: I.89, L.112, N.113, I.114, F.118, M.122, L.125 Chain H: V.9, H.13, F.16, A.17, L.20, I.24 Chain M: I.33, F.44, Y.49 Ligands: 3PE.25 17 PLIP interactions: 6 interactions with chain G, 8 interactions with chain H, 3 interactions with chain M Hydrophobic interactions: G:I.89, G:L.112, G:I.114, G:F.118, G:L.125, H:F.16, H:F.16, H:A.17, H:L.20, H:L.20, H:I.24, M:I.33, M:F.44, M:F.44 Hydrogen bonds: G:N.113, H:H.13 Salt bridges: H:H.13 3PE.16: 26 residues within 4Å: Chain I: L.12, A.19, R.22, G.23, R.115, Y.119, S.126, V.129, L.141, G.145, L.148 Chain J: W.378, M.381, K.382, W.383, A.386, L.389, F.390, M.398, P.399, V.472, V.473, V.476, L.477, F.480 Ligands: 3PE.20 23 PLIP interactions: 11 interactions with chain I, 12 interactions with chain J Hydrophobic interactions: I:L.12, I:L.12, I:R.22, I:V.129, I:L.141, I:L.148, J:W.383, J:A.386, J:L.389, J:F.390, J:V.473, J:V.473, J:V.476, J:L.477, J:F.480 Water bridges: I:R.22, I:R.22, I:R.115, I:R.115, J:W.378, J:A.386 Salt bridges: I:R.115 Hydrogen bonds: J:W.378 3PE.17: 20 residues within 4Å: Chain I: M.168, K.169, V.172, V.173, V.176, F.180, P.234, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, V.430, F.431, V.434, A.438, H.441, R.442 14 PLIP interactions: 4 interactions with chain J, 10 interactions with chain I Hydrophobic interactions: J:F.427, J:V.430, J:V.434, I:K.169, I:V.172, I:V.173, I:V.176, I:V.176, I:P.234, I:F.549, I:V.550, I:V.550, I:F.553 Salt bridges: J:R.442 3PE.18: 12 residues within 4Å: Chain I: L.299, F.363, L.427, R.431, L.511, W.512, V.519, I.522, A.523, G.528, S.532, W.535 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:L.299, I:L.427, I:L.511, I:W.512, I:I.522 Salt bridges: I:R.431 3PE.19: 17 residues within 4Å: Chain I: M.569, A.573, S.576, R.577 Chain J: K.165, T.169, K.173, I.176, Y.177, A.180, I.229, V.233, L.240 Chain K: L.289, V.416, Y.423 Ligands: 3PE.21 18 PLIP interactions: 10 interactions with chain J, 3 interactions with chain I, 5 interactions with chain K Hydrophobic interactions: J:I.176, J:Y.177, J:A.180, J:I.229, J:I.229, J:V.233, J:L.240, I:R.577, K:L.289, K:V.416, K:Y.423, K:Y.423, K:Y.423 Hydrogen bonds: J:T.169, J:T.169 Salt bridges: J:K.165, I:R.577, I:R.577 3PE.20: 11 residues within 4Å: Chain I: I.8, L.12, I.13, L.64, W.65, F.77, V.129, L.141 Chain J: F.480, Y.481 Ligands: 3PE.16 16 PLIP interactions: 10 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:I.8, I:L.12, I:L.12, I:I.13, I:W.65, I:W.65, I:W.65, I:F.77, I:V.129, I:L.141, J:F.480, J:F.480, J:F.480, J:F.480, J:Y.481, J:Y.481 3PE.21: 14 residues within 4Å: Chain J: S.216, S.217, G.218, V.219, Y.221, L.222, L.225, I.229, A.232, L.240, L.293 Ligands: 3PE.19, 3PE.22, LFA.24 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:Y.221, J:L.225, J:L.225, J:I.229, J:A.232, J:L.240, J:L.293 Hydrogen bonds: J:S.216, J:S.216 3PE.22: 16 residues within 4Å: Chain J: V.184, I.187, A.188, A.191, V.195, V.219, L.222, L.223, G.226, I.229 Chain K: H.406, W.408, G.412, V.415 Ligands: 3PE.21, LFA.24 17 PLIP interactions: 10 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:I.187, J:A.188, J:A.191, J:V.195, J:L.222, J:L.222, J:L.223, K:W.408, K:W.408, K:W.408, K:W.408, K:V.415, K:V.415 Water bridges: J:N.198 Salt bridges: K:H.406 3PE.25: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, I.11, I.34, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.15 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: M:A.4, M:I.7, M:I.7, M:I.11, M:I.34, M:L.37, M:L.37, M:F.44 Salt bridges: H:H.13

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

UQ8.13: 14 residues within 4Å: Chain D: F.337 Chain E: W.55, E.84, V.85, L.86 Chain G: S.33, E.36, R.37, D.63, M.64, M.67, F.238, Y.242, R.286 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: G:R.37, G:D.63, G:F.238, G:F.238, E:W.55, E:E.84, E:V.85

3 x LFA: EICOSANE(Non-covalent)

LFA.14: 10 residues within 4Å: Chain G: I.21, V.24, C.28, V.103, S.104, W.107, V.246, P.266, F.268, T.275 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:I.21, G:V.24, G:V.103, G:W.107, G:W.107, G:W.107, G:V.246, G:P.266, G:F.268, G:T.275 LFA.23: 10 residues within 4Å: Chain J: Y.112, F.115, W.122, V.148, W.157 Chain K: F.366, A.374, L.381, M.388, Y.433 11 PLIP interactions: 4 interactions with chain K, 7 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:A.374, K:L.381, J:Y.112, J:Y.112, J:F.115, J:F.115, J:F.115, J:V.148, J:W.157 LFA.24: 7 residues within 4Å: Chain K: F.278, W.408, W.409, G.412, A.413 Ligands: 3PE.21, 3PE.22 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.278, K:W.408, K:W.409, K:W.409

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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