SMTL ID : 8rb9.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 10 residues within 4Å: Chain A: G.23, L.24, C.25, P.26, N.112, C.113 Chain D: A.37, C.39, N.121, C.122 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, Metal complexes: D:C.39, D:C.122, A:C.25, A:C.113

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

LMT.2: 8 residues within 4Å: Chain A: L.5, G.188, L.189, I.190 Chain C: W.312 Chain E: G.129, G.130 Ligands: LMT.8 Ligand excluded by PLIP LMT.3: 4 residues within 4Å: Chain A: E.2, L.5, L.8 Ligands: LMT.8 Ligand excluded by PLIP LMT.8: 6 residues within 4Å: Chain C: R.261, V.304, W.312 Ligands: LMT.2, LMT.3, LMT.9 Ligand excluded by PLIP LMT.9: 6 residues within 4Å: Chain C: M.250, L.253, I.257, Y.262, W.312 Ligands: LMT.8 Ligand excluded by PLIP LMT.11: 7 residues within 4Å: Chain C: F.248, T.252, Y.255, G.264, G.265, L.266 Ligands: LMT.18 Ligand excluded by PLIP LMT.12: 7 residues within 4Å: Chain C: P.31, F.35, V.38, M.39, P.145, P.147, S.209 Ligand excluded by PLIP LMT.13: 6 residues within 4Å: Chain C: W.95, F.164, A.165 Ligands: LMT.14, LMT.15, LMT.21 Ligand excluded by PLIP LMT.14: 5 residues within 4Å: Chain C: F.157, A.161, F.164, A.165 Ligands: LMT.13 Ligand excluded by PLIP LMT.15: 13 residues within 4Å: Chain C: W.95, W.96, F.104, A.130, L.131, A.134, F.135, A.165, G.166 Chain D: I.196, L.198 Ligands: LMT.13, LMT.21 Ligand excluded by PLIP LMT.16: 6 residues within 4Å: Chain C: V.293, I.297, V.300, V.304, W.337 Ligands: LMT.19 Ligand excluded by PLIP LMT.17: 6 residues within 4Å: Chain C: V.230, R.233, W.237, F.279, R.292 Ligands: LMT.18 Ligand excluded by PLIP LMT.18: 11 residues within 4Å: Chain C: E.197, F.200, I.203, L.206, L.223, L.266, L.269, T.270, I.275 Ligands: LMT.11, LMT.17 Ligand excluded by PLIP LMT.19: 6 residues within 4Å: Chain C: I.297, I.333, R.335, Y.336, W.337 Ligands: LMT.16 Ligand excluded by PLIP LMT.21: 6 residues within 4Å: Chain C: W.95 Chain D: P.191, D.192, F.193 Ligands: LMT.13, LMT.15 Ligand excluded by PLIP LMT.22: 9 residues within 4Å: Chain D: G.53, A.99, W.103, M.104, E.106, L.107, S.176, L.177 Ligands: LMT.23 Ligand excluded by PLIP LMT.23: 6 residues within 4Å: Chain D: L.60, M.64, L.95, T.96, W.103 Ligands: LMT.22 Ligand excluded by PLIP

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.4: 12 residues within 4Å: Chain A: P.163, A.164, A.165, F.166 Chain C: L.66, L.103, I.108, Q.111 Chain D: I.207, F.211, V.218, R.221 6 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:R.221, A:A.164, A:A.165 Hydrophobic interactions: C:L.66, C:L.103, C:I.108

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

FMN.5: 18 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, V.267, H.268, N.269, T.272, M.336, I.410, C.412 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.141, B:G.141, B:C.169, B:G.240, B:A.242, B:H.268, B:N.269, B:T.272 Salt bridges: B:K.150 FMN.20: 21 residues within 4Å: Chain C: S.88, 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 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:E.216, C:L.276, C:I.281, C:A.319 Hydrogen bonds: C:R.128, C:A.178, C:L.179, C:G.180, C:S.213, C:S.213, C:G.273, C:A.319, C:A.320 pi-Cation interactions: C:R.128 FMN.24: 14 residues within 4Å: Chain C: 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 14 PLIP interactions: 2 interactions with chain C, 12 interactions with chain E Hydrophobic interactions: C:T.140, C:F.315, E:T.155, E:L.158 Hydrogen bonds: E:E.154, E:T.155, E:T.155, E:T.202, E:I.203, E:T.204, E:T.204 Salt bridges: E:K.190 pi-Stacking: E:Y.128, E:Y.128

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

SF4.6: 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 SF4.7: 12 residues within 4Å: Chain B: C.380, P.381, M.382, L.384, M.389, 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 SF4.25: 13 residues within 4Å: Chain G: A.102, A.118, C.119, T.121, A.123, I.124, C.139, T.140, G.141, C.142, G.143, K.144, C.145 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.119, G:C.139, G:C.142, G:C.145 SF4.26: 11 residues within 4Å: Chain G: Q.108, C.109, I.110, G.111, C.112, T.113, R.114, C.115, V.133, C.149, C.153 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.109, G:C.112, G:C.115, G:C.149

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.10: 21 residues within 4Å: Chain C: I.21, M.22, V.25, S.77, L.80, T.81, L.84, K.110, I.116, G.117, N.119, N.122, P.123, A.124, I.235, F.280, I.281, T.283, D.284, P.285, V.286 11 PLIP interactions: 11 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.122, C:N.122, C:A.124, C:D.284

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
Protein RnfH: F
Ion-translocating oxidoreductase complex subunit B: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
G

F
H

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

Protein RnfH

Ion-translocating oxidoreductase complex subunit B

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