SMTL ID : 9eri.1

Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii bound to NADH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 11 residues within 4Å: Chain A: G.23, I.24, C.25, N.112, C.113 Chain E: G.23, M.24, C.25, V.106, N.107, C.108 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, Metal complexes: E:C.25, E:C.108, A:C.25, A:C.113

10 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)

SF4.2: 11 residues within 4Å: Chain B: C.106, Q.107, A.113, C.138, G.141, C.200, H.201, N.202, C.213, T.215, A.216 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.106, B:C.138, B:C.200, B:C.213 SF4.3: 8 residues within 4Å: Chain B: C.125, C.142, L.143, G.144, G.146, C.148, C.182, M.187 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.125, B:C.142, B:C.148, B:C.182 SF4.4: 8 residues within 4Å: Chain B: C.50, C.53, G.57, C.58, L.61, C.75, P.76, V.77 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.50, B:C.53, B:C.58, B:C.75 SF4.5: 12 residues within 4Å: Chain B: A.102, C.152, F.154, I.157, V.167, C.172, T.173, S.174, C.175, G.176, K.177, C.178 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.152, B:C.172, B:C.175, B:C.178 SF4.6: 10 residues within 4Å: Chain B: C.227, F.229, I.232, I.241, C.246, R.247, Q.248, C.249, Y.250, C.252 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.227, B:C.246, B:C.249, B:C.252 SF4.7: 10 residues within 4Å: Chain B: C.217, I.218, A.219, C.220, G.221, C.223, A.239, C.256, P.257, C.260 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.217, B:C.220, B:C.223, B:C.256, B:C.260 SF4.8: 5 residues within 4Å: Chain B: C.289, P.290, C.310, C.313, C.316 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.289, B:C.313 SF4.9: 9 residues within 4Å: Chain B: I.274, C.279, C.282, G.283, L.284, C.285, Y.303, K.319, C.320 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.279, B:C.282, B:C.282, B:C.320 SF4.12: 10 residues within 4Å: Chain C: C.369, I.370, H.371, C.372, G.373, C.375, L.386, C.418, P.419, L.424 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.369, C:C.372, C:C.375, C:C.418 SF4.13: 12 residues within 4Å: Chain C: C.379, I.381, P.385, C.408, I.409, E.410, C.411, G.412, S.413, C.414, V.425, I.428 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.379, C:C.408, C:C.411, C:C.414

3 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.10: 19 residues within 4Å: Chain C: G.138, L.139, G.140, K.149, N.164, A.166, E.167, C.168, Y.236, G.239, A.240, E.241, V.266, M.267, N.268, T.271, I.409, C.411 Ligands: NAD.11 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.139, C:G.140, C:N.164, C:A.166, C:C.168, C:E.241, C:V.266, C:N.268, C:N.268, C:T.271 FMN.15: 18 residues within 4Å: Chain D: N.89, R.129, L.133, T.143, T.156, P.157, L.158, Y.183, G.184, C.185, E.188, G.238, M.246, P.281, E.282, C.284, S.285, Y.286 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:E.188 Hydrogen bonds: D:T.143, D:L.158, D:S.285 pi-Cation interactions: D:R.129 FMN.16: 15 residues within 4Å: Chain A: L.184, S.187 Chain D: Y.280 Chain E: L.174 Chain F: Y.113, E.139, T.140, L.143, G.144, K.168, G.183, S.184, T.185, I.186, T.187 15 PLIP interactions: 13 interactions with chain F, 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: F:E.139, F:T.140, F:T.140, F:G.144, F:G.183, F:T.185, F:I.186, F:T.187, F:T.187, F:T.187 Salt bridges: F:K.168 pi-Stacking: F:Y.113, F:Y.113 Hydrophobic interactions: E:L.174, A:L.184

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)

NAD.11: 12 residues within 4Å: Chain C: G.140, G.141, A.142, F.144, K.149, E.169, E.241, L.258, P.259, M.335, S.351 Ligands: FMN.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.169 Hydrogen bonds: C:K.149, C:E.241

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.14: 20 residues within 4Å: Chain D: I.23, M.24, V.27, V.81, T.82, L.85, K.111, L.117, G.118, N.120, N.123, P.124, A.125, I.207, F.245, M.246, T.248, D.249, Y.250, A.251 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.23, D:V.27, D:I.207, D:Y.250 Hydrogen bonds: D:T.82, D:N.120, D:N.123, D:A.125, D:D.249, D:D.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery. Nat Commun (2025)

Release Date

2025-03-05

Peptides

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A: A
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B: B
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C: C
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D: D
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E: E
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Membrane

We predict this structure to be a membrane protein.
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Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E

Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G

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