SMTL ID : 8rb8.1

Cryo-EM structure of the NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii, purified with 2-ME/TCEP, 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 A, 2 interactions with chain D, Metal complexes: A:C.25, A:C.113, D:C.39, D:C.122

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

LMT.2: 8 residues within 4Å: Chain A: G.188, L.189, I.190 Chain C: L.305, W.312 Chain E: G.129, G.130 Ligands: LMT.6 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: A:L.189, A:I.190, A:I.190, C:L.305 Hydrogen bonds: A:G.188, E:G.129 LMT.6: 6 residues within 4Å: Chain C: M.250, Y.262, V.308, W.312 Ligands: LMT.2, LMT.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.308, C:W.312, C:W.312 Hydrogen bonds: C:Y.262 Salt bridges: C:R.261 LMT.7: 6 residues within 4Å: Chain C: L.253, A.254, I.257, Y.262, W.312 Ligands: LMT.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.253, C:A.254, C:I.257, C:I.257, C:Y.262, C:W.312 LMT.9: 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:F.248 Hydrogen bonds: C:Y.255, C:L.266 LMT.10: 7 residues within 4Å: Chain C: F.35, V.38, M.39, P.145, P.147, S.209, L.221 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.35, C:F.35, C:V.38, C:M.39, C:L.221 Hydrogen bonds: C:S.209 LMT.11: 7 residues within 4Å: Chain C: V.53, S.54, W.95, F.164 Ligands: LMT.12, LMT.13, LMT.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.53, C:W.95, C:W.95, C:W.95, C:F.164, C:F.164 LMT.12: 3 residues within 4Å: Chain C: F.157, A.161 Ligands: LMT.11 No protein-ligand interaction detected (PLIP) LMT.13: 12 residues within 4Å: Chain C: W.95, G.100, F.104, A.130, A.134, F.135, A.165, G.166 Chain D: Q.194, I.196 Ligands: LMT.11, LMT.16 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:I.196, D:I.196, C:F.104, C:A.130, C:A.134, C:F.135 Hydrogen bonds: D:Q.194, C:A.165, C:A.165 LMT.14: 7 residues within 4Å: Chain C: V.230, L.231, R.233, W.237, V.241, F.279, R.292 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.230, C:L.231, C:W.237, C:V.241, C:F.279 Hydrogen bonds: C:R.292 Salt bridges: C:R.233 LMT.16: 6 residues within 4Å: Chain C: I.58, W.95 Chain D: P.191, D.192 Ligands: LMT.11, LMT.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.58, C:W.95 Hydrogen bonds: D:P.191 LMT.17: 7 residues within 4Å: Chain D: M.100, W.103, M.104, E.106, S.176, L.177 Ligands: LMT.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.177 LMT.18: 5 residues within 4Å: Chain D: L.60, M.64, A.99, W.103 Ligands: LMT.17 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.60 LMT.19: 3 residues within 4Å: Chain A: A.165, F.166 Chain D: F.211 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.211, A:A.165, A:F.166

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

FMN.3: 18 residues within 4Å: Chain B: G.139, G.141, A.143, K.150, N.165, 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 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.410 Hydrogen bonds: B:C.169, B:V.267, B:N.269, B:T.272 Salt bridges: B:K.150 FMN.15: 20 residues within 4Å: Chain C: M.125, R.128, L.132, W.142, T.177, A.178, L.179, G.180, S.213, G.272, G.273, L.276, C.277, I.281, P.316, E.317, A.318, A.319, A.320, F.321 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: 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: 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 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:T.155, E:L.158, C:T.140, C:F.315 Hydrogen bonds: E:E.154, E:T.155, E:T.155, E:T.202, E:I.203, E:T.204, E:T.204 pi-Stacking: E:Y.128, E:Y.128

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

SF4.4: 12 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, L.425 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.370, B:C.373, B:C.376, B:C.419 SF4.5: 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 SF4.21: 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 SF4.22: 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.8: 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 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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