SMTL ID : 7xk3.1

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.1: 18 residues within 4Å: Chain B: I.169, R.209, F.213, W.226, T.236, A.237, L.238, S.271, E.274, G.334, G.335, M.343, P.379, E.380, G.381, M.382, M.383, L.384 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:M.382 Hydrogen bonds: B:A.237, B:L.238, B:S.271, B:E.274, B:G.335, B:E.380, B:E.380, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 pi-Cation interactions: B:R.209 FMN.6: 14 residues within 4Å: Chain B: F.213, P.217, D.223, A.377 Chain C: L.145, W.146, T.173, L.176, G.177, G.223, A.224, T.225, L.226, T.227 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.146, B:F.213, B:P.217 Hydrogen bonds: C:T.173, C:G.177, C:G.223, C:T.225, C:L.226, C:T.227, C:T.227, B:D.223, B:A.377 Salt bridges: C:K.207

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 20 residues within 4Å: Chain B: I.56, M.57, V.60, G.158, V.161, T.162, L.165, K.191, G.198, N.200, N.203, P.204, A.205, I.292, F.342, M.343, T.345, D.346, P.347, V.348 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60, B:P.347 Hydrogen bonds: B:G.158, B:T.162, B:T.162, B:G.198, B:N.200, B:N.203, B:A.205, B:D.346

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

PEE.3: 12 residues within 4Å: Chain B: W.260, M.261, F.264, M.281, I.298, M.302, W.327, H.328, W.329, L.331, F.341 Ligands: LMT.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.260, B:F.264, B:I.298, B:M.302, B:W.327, B:L.331, B:F.341 Hydrogen bonds: B:W.329 Salt bridges: B:H.328 PEE.5: 6 residues within 4Å: Chain B: W.100, L.104, L.123, L.130, Y.133, A.134 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.100, B:L.104, B:L.130, B:L.130, B:Y.133, B:Y.133

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

LMT.4: 8 residues within 4Å: Chain B: M.302, I.306, T.310, N.313, N.324, P.326, W.327 Ligands: PEE.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.306, B:W.327, B:W.327 Hydrogen bonds: B:N.313, B:N.324, B:W.327 LMT.8: 8 residues within 4Å: Chain B: W.177 Chain D: W.174, Y.175, Q.176, N.178, M.181, F.189, L.190 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.189, D:L.190 Hydrogen bonds: D:Q.176, D:Q.176

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

FES.7: 7 residues within 4Å: Chain D: G.27, C.29, C.112 Chain E: G.24, C.26, N.119, C.120 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, Metal complexes: D:C.29, D:C.112, E:C.26 FES.10: 11 residues within 4Å: Chain F: L.56, S.68, A.69, C.70, G.72, G.74, C.76, G.77, Q.78, C.79, C.111 0 PLIP interactions:

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 1 residues within 4Å: Chain E: M.17 No protein-ligand interaction detected (PLIP)

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

FAD.11: 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 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:Y.167, F:A.211, F:F.406, F:F.406 Hydrogen bonds: F:S.213, F:N.227, F:R.229, F:T.232, F:Q.244, F:M.245, F:S.246, F:S.246 Salt bridges: F:R.210, F:R.210 pi-Stacking: F:Y.212, F:F.406, F:F.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishikawa, J.I. et al., Cryo-EM structures of Na + -pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae. Nat Commun (2022)

Release Date

2022-07-20

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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