SMTL ID : 8qby.1

Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs

Coordinates

PDB Format Compare

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)

SF4.1: 11 residues within 4Å: Chain B: H.106, P.107, D.109, C.110, C.113, G.116, C.119, L.121, Q.122, V.210, G.211 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.109 Metal complexes: B:H.106, B:C.110, B:C.113, B:C.119 SF4.2: 13 residues within 4Å: Chain B: M.155, C.158, I.159, S.160, C.161, T.162, R.163, C.164, I.188, C.208, V.210, A.212, L.213 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.158, B:C.161, B:C.164, B:C.208 SF4.5: 13 residues within 4Å: Chain D: H.52, C.74, P.75, A.76, I.79, C.103, I.104, Y.105, C.106, G.107, F.108, C.109, E.120 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:E.120 Metal complexes: D:C.74, D:C.103, D:C.106, D:C.109 SF4.6: 14 residues within 4Å: Chain D: C.64, I.65, A.66, C.67, K.68, L.69, C.70, I.81, Y.96, C.113, P.114, V.115, A.117, I.118 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.64, D:C.67, D:C.70, D:C.113 SF4.24: 12 residues within 4Å: Chain H: I.172, P.190, C.346, G.347, Q.348, C.349, C.352, T.390, I.391, C.392, L.394, G.395 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.346, H:C.349, H:C.352, H:C.392 SF4.34: 14 residues within 4Å: Chain I: R.65, R.85, H.170 Chain P: A.53, C.54, C.55, G.90, T.91, G.117, S.118, C.119, G.148, C.149, P.150 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.54, P:C.55, P:C.119, P:C.149

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

FES.3: 9 residues within 4Å: Chain B: R.35, C.37, Y.38, G.46, N.47, C.48, R.49, C.51, C.66 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.37, B:C.48, B:C.51, B:C.66 FES.10: 11 residues within 4Å: Chain E: C.96, T.98, T.100, C.101, C.137, L.138, G.139, A.140, C.141, M.146 Chain H: P.89 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.96, E:C.101, E:C.137, E:C.141

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain B: Q.115, I.205, C.208, V.210, L.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.115, B:C.208

17 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.7: 7 residues within 4Å: Chain D: G.22, L.23, M.25, R.26, V.29 Chain G: Y.289 Ligands: P5S.8 Ligand excluded by PLIP 3PH.12: 16 residues within 4Å: Chain F: V.415, I.416, F.419, R.423, Y.426, Y.427 Chain Q: I.656, A.660, M.661, I.664 Chain R: I.160, F.164, K.165, L.168, Y.169, L.172 Ligand excluded by PLIP 3PH.15: 16 residues within 4Å: Chain F: M.1, T.2, S.3, F.6, E.12, V.13, A.16, L.20, F.119 Chain K: V.93, W.96, V.100, V.104 Chain L: L.145, Q.148, L.152 Ligand excluded by PLIP 3PH.19: 10 residues within 4Å: Chain G: G.186, D.187, L.191, N.192, L.196, P.197, L.334, G.335, F.337, R.340 Ligand excluded by PLIP 3PH.20: 3 residues within 4Å: Chain G: W.108, W.277 Ligands: 3PH.22 Ligand excluded by PLIP 3PH.22: 8 residues within 4Å: Chain G: W.5, S.14, L.17, Q.18, A.21, A.24 Ligands: 3PH.20, 3PE.21 Ligand excluded by PLIP 3PH.28: 12 residues within 4Å: Chain G: I.75, K.81, F.82, F.85, L.86, F.89 Chain K: I.23, I.26, L.27, A.30, R.35 Ligands: PC1.29 Ligand excluded by PLIP 3PH.30: 10 residues within 4Å: Chain G: F.11, M.15 Chain K: L.5, Y.8, V.13 Chain L: M.1, M.2, F.9, V.45, L.46 Ligand excluded by PLIP 3PH.31: 9 residues within 4Å: Chain A: T.5, H.6, V.9, I.13 Chain L: I.11, C.14, G.105, I.106, S.109 Ligand excluded by PLIP 3PH.35: 15 residues within 4Å: Chain F: V.221, H.224, M.279, L.283, I.286 Chain Q: L.667, A.670, A.671, R.673, V.674, S.676, Y.678, H.681, F.684, A.685 Ligand excluded by PLIP 3PH.36: 14 residues within 4Å: Chain Q: A.167, M.170, K.171, I.174, M.236, L.243, L.244, Y.628, F.632, V.633, K.637 Chain R: L.304, W.436, R.439 Ligand excluded by PLIP 3PH.39: 7 residues within 4Å: Chain Q: R.21 Chain R: P.380, A.381, A.384, R.462, I.469 Ligands: 3PE.38 Ligand excluded by PLIP 3PH.40: 9 residues within 4Å: Chain Q: F.216, W.218, R.219, W.221, N.222, N.225, L.226, F.229, D.287 Ligand excluded by PLIP 3PH.41: 7 residues within 4Å: Chain R: W.36, L.39, L.101, W.104, Q.105, R.460, W.463 Ligand excluded by PLIP 3PH.43: 9 residues within 4Å: Chain F: V.367, L.370, V.374, A.453, L.457 Chain R: L.21, F.22, R.24 Ligands: 3PE.42 Ligand excluded by PLIP 3PH.47: 11 residues within 4Å: Chain R: L.53, F.54, L.87, L.90, L.91, F.94, F.348, M.471, L.481, V.482, V.485 Ligand excluded by PLIP 3PH.48: 7 residues within 4Å: Chain R: F.10, H.69, A.70, W.71, Y.77, L.138, F.139 Ligand excluded by PLIP

2 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.8: 17 residues within 4Å: Chain D: F.28, V.29, S.30, P.31, K.32 Chain G: G.36, K.39, A.43, R.48, I.282, W.285, F.286, Y.289 Chain J: W.21, Y.25 Ligands: 3PH.7, 3PE.17 12 PLIP interactions: 7 interactions with chain G, 4 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: G:K.39, G:A.43, G:W.285, G:Y.289, D:F.28, D:F.28 Water bridges: G:R.48, G:R.48 Salt bridges: G:R.48, D:K.32 Hydrogen bonds: D:K.32, J:Y.25 P5S.37: 19 residues within 4Å: Chain Q: F.301, T.305, L.308, V.309, C.436, F.437, F.440, R.444, T.592, F.596, Y.597, P.604, R.605, L.607, A.608, L.614, Y.615, L.618, W.622 16 PLIP interactions: 16 interactions with chain Q Hydrophobic interactions: Q:F.301, Q:T.305, Q:L.308, Q:F.437, Q:F.437, Q:F.437, Q:F.440, Q:F.440, Q:T.592, Q:F.596, Q:L.607, Q:L.614, Q:L.618, Q:W.622, Q:W.622 Salt bridges: Q:R.444

4 x CA: CALCIUM ION(Non-covalent)

CA.9: 2 residues within 4Å: Chain D: D.88 Chain M: D.48 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain M, 4 Ligand-Water interactions Metal complexes: D:D.88, M:D.48, H2O.32, H2O.33, H2O.33, H2O.33 CA.16: 2 residues within 4Å: Chain F: D.260, L.477 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.260, F:L.477, H2O.16, H2O.16 CA.26: 4 residues within 4Å: Chain I: R.6, N.8, D.49, E.54 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:R.6, I:D.49, I:E.54, I:E.54, H2O.27 CA.49: 2 residues within 4Å: Chain R: L.197, P.275 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:L.197, R:P.275

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

3PE.11: 16 residues within 4Å: Chain F: L.47, A.50, G.54, F.76, V.79, V.80, V.83, A.84, G.87, M.91, T.329, V.333, I.336, A.448, A.469, R.472 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:F.76, F:V.80, F:V.83, F:M.91, F:T.329, F:V.333, F:I.336, F:I.336, F:A.448 Salt bridges: F:R.472 3PE.13: 11 residues within 4Å: Chain F: R.36, T.37, W.40, V.43, A.44, A.45, L.47, V.48, V.83, G.87 Ligands: 3PE.14 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:W.40, F:W.40, F:W.40, F:V.43, F:A.44, F:L.47, F:V.48, F:V.83 Hydrogen bonds: F:T.37, F:T.37 Water bridges: F:T.37, F:T.37 Salt bridges: F:R.36, F:R.36 3PE.14: 10 residues within 4Å: Chain F: V.14, G.17, Y.18, A.21, L.29, R.33, L.34, T.37, L.38 Ligands: 3PE.13 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.18, F:Y.18, F:Y.18, F:A.21, F:T.37, F:L.38 Hydrogen bonds: F:L.29, F:R.33 3PE.17: 14 residues within 4Å: Chain D: N.36 Chain G: F.32, Y.35, R.48, N.51, W.56, L.58, W.285 Chain J: N.17, W.21, L.24, Y.25 Ligands: P5S.8, 3PE.21 15 PLIP interactions: 11 interactions with chain G, 3 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: G:F.32, G:Y.35, G:L.58, G:W.285, G:W.285, G:W.285, G:W.285 Hydrogen bonds: G:N.51, J:N.17, J:W.21, J:Y.25 Water bridges: G:R.48, G:R.48, D:N.36 Salt bridges: G:R.48 3PE.21: 17 residues within 4Å: Chain G: Q.18, A.21, V.22, A.24, F.25, S.29, F.32, F.104, G.107, W.108, V.109, M.110, W.277, W.285 Chain K: E.7 Ligands: 3PE.17, 3PH.22 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: G:V.22, G:A.24, G:F.25, G:F.32, G:W.108, G:W.277, G:W.277, G:W.285 Hydrogen bonds: G:Q.18, G:Q.18, K:E.7 Water bridges: G:S.14 3PE.27: 11 residues within 4Å: Chain G: L.59, F.62 Chain J: L.5, L.8, T.9, W.11, N.12 Chain P: D.35, I.36, W.39, R.168 8 PLIP interactions: 3 interactions with chain G, 2 interactions with chain J, 3 interactions with chain P Hydrophobic interactions: G:L.59, G:F.62, G:F.62, J:L.8, P:W.39, P:W.39 Hydrogen bonds: J:N.12, P:R.168 3PE.38: 19 residues within 4Å: Chain Q: G.17, L.18, W.20, R.21, H.113, R.117, Y.121, F.124, Y.160 Chain R: V.376, A.383, A.384, M.387, F.388, M.391, L.396, Y.438, L.473 Ligands: 3PH.39 15 PLIP interactions: 6 interactions with chain R, 9 interactions with chain Q Hydrophobic interactions: R:A.384, R:F.388, R:F.388, R:M.391, R:L.396, R:L.473, Q:L.18, Q:Y.121, Q:F.124 Hydrogen bonds: Q:H.113, Q:H.113 Water bridges: Q:R.117 Salt bridges: Q:R.21, Q:R.117, Q:R.117 3PE.42: 18 residues within 4Å: Chain F: P.366, V.367, L.370, L.373, V.374, T.385, L.457 Chain R: I.17, A.20, L.21, R.24, K.111, E.112, I.115, A.116, I.145, L.149 Ligands: 3PH.43 18 PLIP interactions: 7 interactions with chain F, 11 interactions with chain R Hydrophobic interactions: F:P.366, F:L.370, F:L.373, F:V.374, F:T.385, F:L.457, R:I.17, R:I.17, R:A.20, R:E.112, R:I.115, R:I.145, R:L.149 Hydrogen bonds: F:V.367, R:K.111, R:K.111 Salt bridges: R:R.24, R:K.111 3PE.44: 13 residues within 4Å: Chain F: V.399, D.400, G.402, W.405, I.412 Chain R: L.176, A.183, M.217, L.220, L.221, L.223, A.224, A.227 7 PLIP interactions: 4 interactions with chain R, 3 interactions with chain F Hydrophobic interactions: R:L.176, R:L.220, R:L.223, R:A.227, F:I.412 Hydrogen bonds: F:V.399, F:D.400 3PE.45: 10 residues within 4Å: Chain R: L.208, M.211, T.212, V.213, V.214, L.223, F.226, V.283, A.284, Y.287 8 PLIP interactions: 8 interactions with chain R Hydrophobic interactions: R:L.208, R:L.223, R:L.223, R:F.226, R:A.284, R:Y.287, R:Y.287 Hydrogen bonds: R:Y.287

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 15 residues within 4Å: Chain F: Y.28 Chain G: R.308, K.312, V.313, P.316, L.317, G.320, W.321 Chain K: T.106, F.109, A.110, W.113, K.114 Chain L: N.176, L.178 15 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F, 7 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: G:P.316, G:W.321, F:Y.28, K:T.106, K:F.109, K:W.113, K:W.113, K:W.113 Hydrogen bonds: G:K.312, G:K.312, L:N.176 Salt bridges: G:R.308, G:K.312, K:K.114, K:K.114 CDL.46: 5 residues within 4Å: Chain R: P.286, W.290, L.291, I.294, W.418 7 PLIP interactions: 7 interactions with chain R Hydrophobic interactions: R:W.290, R:W.290, R:W.290, R:W.290, R:L.291, R:I.294, R:W.418

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.23: 18 residues within 4Å: Chain H: G.54, R.55, G.56, K.65, N.83, D.85, E.86, S.87, Y.171, G.174, E.175, E.176, V.209, N.210, N.211, S.214, A.393, L.394 22 PLIP interactions: 22 interactions with chain H Hydrophobic interactions: H:Y.171, H:Y.171, H:E.175, H:E.175, H:A.393, H:L.394 Hydrogen bonds: H:G.56, H:N.83, H:E.86, H:S.87, H:G.174, H:E.176, H:N.210, H:N.211, H:N.211, H:S.214 Water bridges: H:G.59, H:G.59, H:K.65, H:N.83, H:D.94 Salt bridges: H:K.65

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.25: 20 residues within 4Å: Chain D: Y.11, F.12, L.13, M.14, F.17, I.18, F.21 Chain G: V.203, V.207, P.217, F.218, M.290, V.294, Y.301, R.308, I.309, V.313 Chain I: R.213, Q.217 Chain L: M.181 15 PLIP interactions: 2 interactions with chain I, 6 interactions with chain D, 7 interactions with chain G Hydrogen bonds: I:Q.217, G:Y.301 Salt bridges: I:R.213, G:R.308 Hydrophobic interactions: D:F.17, D:F.17, D:I.18, D:F.21, D:F.21, D:F.21, G:V.203, G:V.203, G:P.217, G:V.294 Water bridges: G:R.308 PC1.29: 13 residues within 4Å: Chain G: D.80, F.82, L.86, L.90, L.94, F.97 Chain L: R.24, N.25, H.28, L.31, W.32, I.34 Ligands: 3PH.28 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain L Hydrophobic interactions: G:F.82, G:L.86, G:L.90, G:L.94, G:F.97, L:L.31, L:W.32, L:I.34 Salt bridges: L:H.28, L:H.28

1 x ZN: ZINC ION(Non-covalent)

ZN.32: 5 residues within 4Å: Chain M: C.18, G.20, H.28, C.44, C.47 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.18, M:H.28, M:C.44, M:C.47

1 x U10: UBIQUINONE-10(Non-covalent)

U10.33: 17 residues within 4Å: Chain G: M.27, I.31, V.34, R.38, W.41, T.61, D.64, A.65, Y.68, L.241, M.244, A.245, K.295 Chain P: H.46, E.70, A.75, R.77 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain P Hydrophobic interactions: G:I.31, G:V.34, G:T.61, G:D.64, G:A.65, G:Y.68, G:L.241 Hydrogen bonds: G:K.295, P:R.77, P:R.77 pi-Cation interactions: P:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ivanov, B.S. et al., Structure of the turnover-ready state of an ancestral respiratory complex I. Nat Commun (2024)

Release Date

2024-09-11

Peptides

NADH-quinone oxidoreductase subunit K: A
NADH-quinone oxidoreductase: B
Protein-L-isoaspartate O-methyltransferase: C
NADH-quinone oxidoreductase subunit I: D
NADH dehydrogenase subunit E: E
NADH-quinone oxidoreductase subunit N: F
NADH-quinone oxidoreductase subunit H: G
NADH-quinone oxidoreductase subunit F: H
NADH-quinone oxidoreductase subunit D: I
NADH:ubiquinone oxidoreductase 17.2 kD subunit: J
NADH-quinone oxidoreductase subunit A: K
NADH-quinone oxidoreductase chain 10: L
Zinc finger CHCC-type domain-containing protein: M
ETC complex I subunit conserved region: N
NADH-quinone oxidoreductase subunit C: O
NADH-quinone oxidoreductase subunit B: P
NADH dehydrogenase subunit L: Q
NADH dehydrogenase subunit M: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
G

C
t

D
I

E
E

F
N

G
H

H
F

I
D

J
q

K
A

L
J

M
R

N
Q

O
C

P
B

Q
L

R
M

Membrane

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

NADH-quinone oxidoreductase

Protein-L-isoaspartate O-methyltransferase

NADH-quinone oxidoreductase subunit I

NADH dehydrogenase subunit E

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit D

NADH:ubiquinone oxidoreductase 17.2 kD subunit

NADH-quinone oxidoreductase subunit A

NADH-quinone oxidoreductase chain 10

Zinc finger CHCC-type domain-containing protein

ETC complex I subunit conserved region

NADH-quinone oxidoreductase subunit C

NADH-quinone oxidoreductase subunit B

NADH dehydrogenase subunit L

NADH dehydrogenase subunit M

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