SMTL ID : 8rbm.1

Cryo-EM structure of the NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii, ferricyanide oxidized

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-2-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: G.23, L.24, C.25, P.26, N.112, C.113 Chain D: A.37, C.39, C.122 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, Metal complexes: A:C.25, A:C.113, D:C.39, D:C.122

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

LMT.2: 10 residues within 4Å: Chain A: L.5, G.188, L.189, I.190 Chain C: W.312 Chain E: G.129, G.130, P.131 Ligands: LMT.3, LMT.7 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:G.129 Hydrophobic interactions: A:L.5, A:I.190 LMT.3: 6 residues within 4Å: Chain A: E.2, V.4, L.5 Ligands: LMT.2, LMT.7, LMT.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.4, A:L.5 Hydrogen bonds: A:E.2, A:E.2 LMT.7: 6 residues within 4Å: Chain C: R.261, Y.262, W.312 Ligands: LMT.2, LMT.3, LMT.8 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.312, C:W.312 Hydrogen bonds: C:R.261 LMT.8: 7 residues within 4Å: Chain C: M.250, L.253, A.254, I.257, W.312 Ligands: LMT.3, LMT.7 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.253, C:A.254, C:I.257, C:W.312 LMT.10: 7 residues within 4Å: Chain C: L.196, F.248, T.252, Y.255, G.264, G.265, L.266 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.248, C:T.252 Hydrogen bonds: C:Y.255, C:L.266 LMT.11: 6 residues within 4Å: Chain C: F.35, V.38, M.39, P.145, P.147, S.209 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.35, C:V.38 Hydrogen bonds: C:S.209 LMT.12: 6 residues within 4Å: Chain C: W.95, F.164, A.165 Ligands: LMT.13, LMT.14, LMT.19 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.95, C:W.95, C:F.164 LMT.13: 4 residues within 4Å: Chain C: F.157, A.161, F.164 Ligands: LMT.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.164, C:F.164 LMT.14: 16 residues within 4Å: Chain C: W.95, W.96, G.100, F.104, A.130, L.131, A.134, F.135, A.165, G.166 Chain D: F.193, Q.194, I.196, L.198 Ligands: LMT.12, LMT.19 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.104, C:A.130, C:L.131, C:A.134, C:F.135, D:I.196, D:I.196, D:L.198 Hydrogen bonds: C:A.165, C:A.165 LMT.15: 6 residues within 4Å: Chain C: R.292, V.293, I.297, G.301, M.326, W.337 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.297 Hydrogen bonds: C:R.292 LMT.16: 8 residues within 4Å: Chain C: L.223, V.230, R.233, W.237, V.241, L.244, F.279, R.292 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.223, C:W.237, C:V.241, C:L.244, C:F.279 Hydrogen bonds: C:R.233, C:R.233 LMT.19: 6 residues within 4Å: Chain D: I.190, P.191, D.192, F.193 Ligands: LMT.12, LMT.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.191

3 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)(Covalent)

FMN.4: 17 residues within 4Å: Chain B: G.139, G.141, K.150, N.165, S.167, E.168, C.169, Y.237, G.240, S.241, A.242, H.268, N.269, T.272, M.336, I.410, C.412 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.410 Hydrogen bonds: B:G.141, B:C.169, B:G.240, B:N.269, B:T.272 Salt bridges: B:K.150 FMN.17: 20 residues within 4Å: Chain C: M.125, R.128, L.132, W.142, T.177, A.178, L.179, G.180, S.213, E.216, G.272, G.273, L.276, I.281, P.316, E.317, A.318, A.319, A.320, F.321 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:E.216, C:L.276, C:I.281, C:A.319 Hydrogen bonds: C:A.178, C:L.179, C:G.180, C:S.213, C:S.213, C:G.273, C:A.320 pi-Cation interactions: C:R.128 FMN.20: 15 residues within 4Å: Chain C: L.132, T.140, F.315, P.316 Chain E: Y.128, E.154, T.155, L.158, A.159, K.190, G.200, A.201, T.202, I.203, T.204 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:T.155, E:L.158, C:L.132, C:T.140, C:F.315 Hydrogen bonds: E:T.155, E:T.202, E:I.203, E:T.204, E:T.204 pi-Stacking: E:Y.128

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

SF4.5: 11 residues within 4Å: Chain B: C.370, I.371, R.372, C.373, A.374, S.375, C.376, V.418, C.419, P.420, S.421 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.370, B:C.373, B:C.376, B:C.419 SF4.6: 11 residues within 4Å: Chain B: C.380, P.381, M.382, L.384, C.409, I.410, L.411, C.412, G.413, C.414, C.415 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.380, B:C.409, B:C.412, B:C.415

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.9: 20 residues within 4Å: Chain C: I.21, M.22, V.25, S.77, L.80, T.81, L.84, K.110, G.117, N.119, N.122, P.123, A.124, I.235, F.280, I.281, T.283, D.284, P.285, V.286 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.21, C:V.25, C:L.80, C:I.235 Hydrogen bonds: C:S.77, C:G.117, C:N.119, C:N.119, C:N.122, C:N.122, C:A.124, C:D.284, C:D.284

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Covalent)

PTY.18: 10 residues within 4Å: Chain A: A.165, F.166 Chain C: L.66, L.103, I.108 Chain D: I.161, L.165, F.211, A.215, R.221 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.66, C:L.103, C:I.108, D:I.161, D:L.165, D:F.211, D:F.211, D:A.215 Hydrogen bonds: D:R.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat.Chem.Biol. (2024)

Release Date

2024-06-26

Peptides

Ion-translocating oxidoreductase complex subunit A: A
Ion-translocating oxidoreductase complex subunit C: B
Ion-translocating oxidoreductase complex subunit D: C
Ion-translocating oxidoreductase complex subunit E: D
Ion-translocating oxidoreductase complex subunit G: E
Ion-translocating oxidoreductase complex subunit B: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
G

F
B

G
b

Membrane

We predict this structure to be a membrane protein.
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Ion-translocating oxidoreductase complex subunit A

Ion-translocating oxidoreductase complex subunit C

Ion-translocating oxidoreductase complex subunit D

Ion-translocating oxidoreductase complex subunit E

Ion-translocating oxidoreductase complex subunit G

Ion-translocating oxidoreductase complex subunit B

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