SMTL ID : 8rbq.1

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

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: 7 residues within 4Å: Chain A: C.25, P.26, N.112, C.113 Chain C: A.37, C.39, C.122 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, Metal complexes: C:C.39, C:C.122, A:C.25, A:C.113

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

LMT.2: 8 residues within 4Å: Chain A: L.12, G.188, L.189, I.190 Chain D: I.126 Chain G: L.305, W.312 Ligands: LMT.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:L.12, A:L.189, A:I.190, G:L.305 LMT.6: 12 residues within 4Å: Chain C: F.193, Q.194 Chain G: W.96, G.100, F.104, A.130, L.131, A.134, F.135, Q.138, G.166 Ligands: PTY.12 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain G Hydrogen bonds: C:Q.194, G:Q.138 Hydrophobic interactions: G:W.96, G:F.104, G:L.131, G:A.134, G:F.135, G:F.135 LMT.10: 6 residues within 4Å: Chain G: R.261, Y.262, V.308, W.312 Ligands: LMT.2, LMT.11 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:W.312 Hydrogen bonds: G:R.261 Salt bridges: G:R.261 LMT.11: 6 residues within 4Å: Chain G: M.250, L.253, N.258, Y.262, W.312 Ligands: LMT.10 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.253, G:W.312 Hydrogen bonds: G:N.258 LMT.14: 4 residues within 4Å: Chain G: W.95, F.164, A.165 Ligands: LMT.15 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:W.95, G:F.164, G:F.164 LMT.15: 4 residues within 4Å: Chain G: F.157, A.161, F.164 Ligands: LMT.14 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.164, G:F.164 LMT.16: 12 residues within 4Å: Chain G: G.36, L.37, F.40, A.44, A.86, I.87, P.91, W.142, A.143, G.272, G.273, L.276 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.37, G:F.40, G:F.40, G:A.44, G:L.276 Hydrogen bonds: G:G.272, G:G.273

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

FMN.3: 16 residues within 4Å: Chain B: G.139, G.141, K.150, N.165, C.169, E.170, G.240, S.241, A.242, V.267, H.268, N.269, T.272, M.336, I.410, C.412 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.410 Hydrogen bonds: B:G.141, B:A.143, B:N.165, B:C.169, B:V.267, B:N.269, B:T.272 Salt bridges: B:K.150, B:H.268 FMN.7: 13 residues within 4Å: Chain D: Y.128, E.154, T.155, L.158, A.159, K.190, G.200, A.201, T.202, I.203, T.204 Chain G: I.133, F.315 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain D Hydrophobic interactions: G:I.133, G:F.315, D:T.155 Hydrogen bonds: D:E.154, D:T.155, D:T.202, D:I.203, D:T.204, D:T.204 Salt bridges: D:K.190 pi-Stacking: D:Y.128

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

SF4.4: 10 residues within 4Å: Chain B: C.370, I.371, R.372, C.373, A.374, C.376, L.387, 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 SF4.5: 14 residues within 4Å: Chain B: C.380, P.381, M.382, L.384, P.386, M.389, C.409, I.410, L.411, C.412, G.413, C.414, C.415, F.429 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.380, B:C.409, B:C.412, B:C.415 SF4.8: 13 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.119, F:C.139, F:C.142, F:C.145 SF4.9: 9 residues within 4Å: Chain F: C.109, G.111, C.112, T.113, R.114, C.115, V.133, C.149, C.153 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.109, F:C.112, F:C.115, F:C.149

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.12: 13 residues within 4Å: Chain A: P.163, A.165, F.166 Chain C: V.208, F.211, A.215, V.218, R.221 Chain G: L.66, L.103, I.108, L.112 Ligands: LMT.6 8 PLIP interactions: 3 interactions with chain G, 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: G:L.66, G:I.108, G:L.112, C:V.208, C:F.211, C:A.215 Hydrogen bonds: A:A.164, C:R.221 PTY.17: 6 residues within 4Å: Chain G: L.223, V.227, V.230, W.237, V.241, F.279 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:L.223, G:V.227, G:V.241, G:F.279 Hydrogen bonds: G:V.230

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.13: 21 residues within 4Å: Chain G: 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 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.21, G:L.80, G:I.235 Hydrogen bonds: G:S.77, G:G.117, G:N.119, G:N.122, G:A.124

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
H

F
B

G
D

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 E

Ion-translocating oxidoreductase complex subunit G

Protein RnfH

Ion-translocating oxidoreductase complex subunit B

Ion-translocating oxidoreductase complex subunit D

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