SMTL ID : 9erl.1

Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii in apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NA.1: 3 residues within 4Å: Chain A: L.18, A.180, L.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.18 NA.2: 4 residues within 4Å: Chain A: L.18, S.19, F.21 Chain E: P.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.19 NA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

FES.3: 9 residues within 4Å: Chain A: L.22, C.25, T.111, N.112, C.113 Chain E: G.23, C.25, 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)

SF4.4: 8 residues within 4Å: Chain B: C.106, Q.107, A.113, C.138, C.200, H.201, C.213, A.216 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.106, B:C.138, B:C.200, B:C.213 SF4.5: 10 residues within 4Å: Chain B: C.125, C.142, L.143, G.144, Y.145, G.146, T.147, 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 SF4.6: 9 residues within 4Å: Chain B: P.46, G.47, N.49, C.50, G.52, C.53, C.58, C.75, V.77 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.50, B:C.53, B:C.58, B:C.75 SF4.7: 8 residues within 4Å: Chain B: C.152, F.154, I.157, C.172, T.173, C.175, 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 SF4.8: 9 residues within 4Å: Chain B: C.227, F.229, I.232, C.246, R.247, Q.248, C.249, Y.250, C.252 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.227, B:C.246, B:C.252 SF4.9: 9 residues within 4Å: Chain B: C.217, I.218, A.219, C.220, G.221, C.223, A.239, C.256, P.257 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.217, B:C.220, B:C.223, B:C.256 SF4.10: 7 residues within 4Å: Chain B: C.289, V.291, C.310, G.312, C.313, C.316, M.327 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.289, B:C.310, B:C.313, B:C.316 SF4.11: 7 residues within 4Å: Chain B: C.279, C.282, G.283, L.284, C.285, C.320, R.321 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.279, B:C.282, B:C.285, B:C.320 SF4.12: 8 residues within 4Å: Chain C: C.369, I.370, H.371, C.372, G.373, C.375, C.418, P.419 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.369, C:C.372, C:C.375, C:C.418 SF4.13: 11 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, 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(Non-covalent)(Covalent)

FMN.14: 16 residues within 4Å: Chain C: G.138, L.139, G.140, K.149, N.164, A.166, E.167, C.168, G.239, A.240, E.241, V.266, M.267, N.268, T.271, M.335 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.240 Hydrogen bonds: C:L.139, C:G.140, C:N.164, C:C.168, C:A.240, C:N.268, C:T.271 Salt bridges: C:K.149 FMN.15: 14 residues within 4Å: Chain D: N.89, R.129, Y.145, T.156, L.158, A.159, C.185, E.188, G.237, G.238, P.281, E.282, S.285, Y.286 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:E.188 Hydrogen bonds: D:R.129, D:A.159, D:C.185, D:E.188, D:G.238, D:E.282, D:E.282, D:S.285 pi-Cation interactions: D:R.129 FMN.18: 12 residues within 4Å: 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 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Y.113, F:L.143, E:L.174 Hydrogen bonds: F:T.140, F:T.140, F:T.185, F:I.186, F:T.187, F:T.187 Salt bridges: F:K.168 pi-Stacking: F:Y.113, F:Y.113

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.16: 16 residues within 4Å: Chain D: I.23, S.78, V.81, T.82, L.85, L.117, G.118, N.120, N.123, P.124, A.125, F.245, M.246, T.248, D.249, Y.250 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.23, D:Y.250 Hydrogen bonds: D:S.78, D:G.118, D:N.120, D:N.123, 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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