SMTL ID : 8ahx.1

Cryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii

Coordinates

PDB Format

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 E: A.37, C.39, N.121, C.122 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, Metal complexes: E:C.39, E:C.122, A:C.25, A:C.113

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

LMT.2: 8 residues within 4Å: Chain A: G.188, L.189, I.190 Chain D: W.312 Chain F: G.129, G.130 Ligands: LMT.3, LMT.9 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.129 LMT.3: 7 residues within 4Å: Chain A: E.2, V.4, L.5, L.8 Ligands: LMT.2, LMT.9, LMT.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.4, A:L.5, A:L.5, A:L.8 Hydrogen bonds: A:E.2, A:E.2 LMT.9: 6 residues within 4Å: Chain D: R.261, Y.262, W.312 Ligands: LMT.2, LMT.3, LMT.10 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.312, D:W.312 LMT.10: 7 residues within 4Å: Chain D: M.250, L.253, A.254, I.257, W.312 Ligands: LMT.3, LMT.9 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.253, D:A.254, D:I.257, D:W.312 Hydrogen bonds: D:Y.262 LMT.12: 7 residues within 4Å: Chain D: L.196, F.248, T.252, Y.255, G.264, G.265, L.266 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.248, D:F.248, D:T.252 Hydrogen bonds: D:Y.255, D:L.266 LMT.13: 7 residues within 4Å: Chain D: P.31, F.35, V.38, M.39, P.145, P.147, S.209 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.35, D:V.38, D:M.39 Hydrogen bonds: D:S.209 LMT.14: 6 residues within 4Å: Chain D: W.95, F.164, A.165 Ligands: LMT.15, LMT.16, LMT.23 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.95, D:W.95, D:W.95, D:F.164, D:F.164 LMT.15: 3 residues within 4Å: Chain D: A.161, F.164 Ligands: LMT.14 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.164 LMT.16: 13 residues within 4Å: Chain D: W.95, W.96, G.100, F.104, A.130, A.134, F.135, A.165, G.166 Chain E: Q.194, I.196 Ligands: LMT.14, LMT.23 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.104, D:A.130, D:A.134, D:F.135, E:I.196 Hydrogen bonds: D:A.165, D:A.165, E:Q.194 LMT.17: 3 residues within 4Å: Chain D: V.293, G.301, W.337 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.337 LMT.18: 5 residues within 4Å: Chain D: L.223, V.230, R.233, W.237, R.292 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.223, D:W.237 Hydrogen bonds: D:R.233, D:R.233, D:R.292 LMT.20: 6 residues within 4Å: Chain E: M.100, M.104, E.106, S.176, L.177 Ligands: LMT.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.177 LMT.21: 6 residues within 4Å: Chain E: L.60, M.64, T.96, A.99, W.103 Ligands: LMT.20 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.60, E:A.99, E:W.103 LMT.22: 5 residues within 4Å: Chain A: A.165 Chain D: L.65, L.66 Chain E: F.211, A.215 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: A:A.165, E:F.211, E:A.215 Hydrogen bonds: D:L.66 LMT.23: 5 residues within 4Å: Chain D: V.99 Chain E: P.191, D.192 Ligands: LMT.14, LMT.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.99 Hydrogen bonds: E:P.191

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

SF4.4: 13 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.119, B:C.139, B:C.142, B:C.145 SF4.5: 11 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.109, B:C.112, B:C.115, B:C.149 SF4.7: 11 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.370, C:C.373, C:C.376, C:C.419 SF4.8: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.380, C:C.409, C:C.412, C:C.415

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

FMN.6: 16 residues within 4Å: Chain C: 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 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.410 Hydrogen bonds: C:G.141, C:C.169, C:E.170, C:V.267, C:N.269, C:T.272 Salt bridges: C:K.150 FMN.19: 20 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:E.216, D:L.276, D:I.281, D:A.319 Hydrogen bonds: D:A.178, D:L.179, D:G.180, D:S.213, D:S.213, D:G.273, D:A.320 pi-Cation interactions: D:R.128 FMN.24: 14 residues within 4Å: Chain D: T.140, F.315, P.316 Chain F: Y.128, E.154, T.155, L.158, A.159, K.190, G.200, A.201, T.202, I.203, T.204 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.158, D:T.140, D:F.315 Hydrogen bonds: F:E.154, F:T.155, F:T.155, F:T.202, F:I.203, F:T.204, F:T.204 pi-Stacking: F:Y.128, F:Y.128

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.11: 20 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:I.21, D:V.25, D:L.80, D:I.235 Hydrogen bonds: D:S.77, D:G.117, D:N.119, D:N.122, D:N.122, D:A.124, D:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Architecture of the NADH:ferredoxin oxidoreductase RNF that drives Biological Nitrogen Fixation. To Be Published

Release Date

2023-11-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

G
H

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 B

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