SMTL ID : 9udg.1

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.18 Å

Oligo State

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

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain B: I.169, R.209, F.213, W.226, T.236, A.237, L.238, S.239, S.271, E.274, G.334, G.335, M.343, P.379, E.380, G.381, M.382, M.383, L.384 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:M.382, B:M.383 Hydrogen bonds: B:T.236, B:T.236, B:L.238, B:S.239, B:S.271, B:E.274, B:G.335, B:E.380, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 Water bridges: B:T.236, B:A.237, B:S.239 pi-Cation interactions: B:R.209 FMN.7: 18 residues within 4Å: Chain B: F.213, P.217, S.221, G.222, D.223, A.377 Chain C: L.145, W.146, E.172, T.173, L.176, G.177, K.207, G.223, A.224, T.225, L.226, T.227 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:F.213, B:P.217, C:W.146 Hydrogen bonds: B:G.222, B:D.223, C:T.173, C:T.173, C:G.177, C:T.225, C:T.225, C:T.225, C:L.226, C:T.227, C:T.227 Water bridges: B:D.223, C:A.224 Salt bridges: C:K.207

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 18 residues within 4Å: Chain B: I.56, V.60, V.161, T.162, L.165, T.197, G.198, N.200, N.203, P.204, A.205, I.292, F.342, M.343, T.345, D.346, P.347, V.348 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60, B:I.292 Hydrogen bonds: B:T.162, B:G.198, B:N.200, B:N.203, B:N.203, B:A.205, B:D.346

1 x 0NI: Aurachin D(Non-covalent)

0NI.3: 14 residues within 4Å: Chain A: W.337 Chain B: L.26, A.29, L.33, K.54, F.137, G.141, V.145, V.155, N.156, E.157, G.158, F.159, F.160 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.26, B:A.29, B:L.33, B:L.33, B:K.54, B:F.137, B:V.145, B:V.155, B:E.157, B:F.159, B:F.159, B:F.160, A:W.337 Hydrogen bonds: B:G.158, B:F.159, B:F.160 Water bridges: B:K.54 pi-Stacking: B:F.160, B:F.160

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.4: 12 residues within 4Å: Chain B: W.260, M.261, M.281, A.285, W.295, I.298, M.302, H.328, W.329, L.331, F.341 Ligands: LMT.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.260, B:W.295, B:I.298, B:L.331, B:F.341 Salt bridges: B:H.328 PEE.6: 6 residues within 4Å: Chain B: W.100, L.108, L.130, P.131, T.135, L.176 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.100, B:P.131, B:L.176

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.5: 7 residues within 4Å: Chain B: I.306, T.310, N.313, N.324, P.326, W.327 Ligands: PEE.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.306, B:I.306, B:T.310, B:W.327 Hydrogen bonds: B:N.324 LMT.9: 7 residues within 4Å: Chain B: W.177, L.181, Y.216 Chain D: W.174, Y.175, Q.176, M.181 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.176, D:Q.176 Hydrophobic interactions: B:L.181

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain C: Q.93, R.118, A.119, H.141 No protein-ligand interaction detected (PLIP)

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

FES.10: 8 residues within 4Å: Chain D: G.27, V.28, C.29, C.112 Chain E: G.24, M.25, C.26, C.120 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, Metal complexes: D:C.29, D:C.112, E:C.26, E:C.120 FES.11: 8 residues within 4Å: Chain F: S.68, C.70, G.73, G.74, S.75, C.76, G.77, C.79 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.70, F:G.73, F:C.79

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 19 residues within 4Å: Chain F: Y.167, R.210, A.211, Y.212, S.213, N.227, V.228, R.229, A.231, T.232, P.233, P.234, V.240, P.241, G.243, Q.244, M.245, S.246, F.406 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.167, F:A.211, F:F.406 Hydrogen bonds: F:A.211, F:A.211, F:S.213, F:N.227, F:R.229, F:P.241, F:Q.244, F:M.245, F:S.246 Salt bridges: F:R.210, F:R.210 pi-Stacking: F:F.406, F:F.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishikawa-Fukuda, M. et al., The Na + -pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes. Biorxiv (2025)

Release Date

2025-06-25

Peptides

Na(+)-translocating NADH-quinone reductase subunit A: A
Na(+)-translocating NADH-quinone reductase subunit B: B
Na(+)-translocating NADH-quinone reductase subunit C: C
Na(+)-translocating NADH-quinone reductase subunit D: D
Na(+)-translocating NADH-quinone reductase subunit E: E
Na(+)-translocating NADH-quinone reductase subunit F: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Na(+)-translocating NADH-quinone reductase subunit A

Na(+)-translocating NADH-quinone reductase subunit B

Na(+)-translocating NADH-quinone reductase subunit C

Na(+)-translocating NADH-quinone reductase subunit D

Na(+)-translocating NADH-quinone reductase subunit E

Na(+)-translocating NADH-quinone reductase subunit F

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