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Architecture of the RNF1 complex that drives biological nitrogen fixation

Abstract

Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron–sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.

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Fig. 1: The nitrogenase-associated RNF1 complex from A. vinelandii.
Fig. 2: Tracing the path of an electron through the RNF complex.
Fig. 3: Electron transfer to the acceptor ferredoxin.
Fig. 4: Predicted and experimental structures of complexes of the RNF/NQR family.
Fig. 5: Functional properties of RNF.

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Data availability

The data that support the findings of this study are available within the main text and its extended data files. The atomic coordinates and the masked, unsharpened and sharpened maps post-processing for the A. vinelandii RNF complex have been deposited in the Protein Data Bank at http://www.pdb.org with accession codes 8AHX/EMD-15452 (native), 8RB9/EMD-19029 (NADH), 8RB8/EMD-19028 (NADH+β-ME/TCEP), 8RBQ/EMD-19034 (NADH+Na2S2O4) and 8RBM/EMD-19032 (K3Fe(CN)6). Source data are provided as a Source Data file. Data are also available from the corresponding author upon reasonable request. Source data are provided with this paper.

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Acknowledgements

This work was supported by the European Research Council (grant no. 310656 to O.E.) and the Deutsche Forschungsgemeinschaft to O.E. (CRC 1381, project ID 403222702; CRC 992, project ID 192904750; and RTG 2202, project ID 278002225). We acknowledge the bwHPC Cluster of the federal state of Baden-Württemberg and the Deutsche Forschungsgemeinschaft (grant INST 35/134-1 FUGG) for computational support. The authors thank G. Fritz, J. Steuber and T. Friedrich for stimulating discussions; P. Dos Santos for support with genetic modifications in A. vinelandii; and M. Chami at the Bio-EM facility of Basel University Biocenter for excellent assistance with cryo-EM data collection.

Author information

Authors and Affiliations

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Contributions

L.Z. and O.E. designed the research. L.Z. conducted the experiments and collected data. L.Z. built and refined the structural models. L.Z. and O.E. evaluated the data and wrote the manuscript.

Corresponding author

Correspondence to Oliver Einsle.

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Nature Chemical Biology thanks Blanca Barquera and the other, anonymous reviewers for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Production and characteristics of the RNF complex.

(A) Generation of a Δfix strain of A. vinelandii through insertion of a chloramphenicol resistance cassette by a double crossover. (B) Generation of the strain containing a StrepTag(II) coding sequencing at the C-terminus of RnfG by single crossover into the A. vinelandii Δfix genome. (C) Size-exclusion chromatography (SEC) profile. The fractions highlighted in yellow contained the RNF complex. (D) UV-vis spectra of the purified RNF complex with the combined absorption features of flavin cofactors and iron-sulfur clusters. (E) SDS-PAGE analysis of the complex. Lane 1, Coomassie blue stained gel; lane 2, the unstained gel under UV illumination showed the covalently bound FMN in RnfD and RnfG. The calculated molecular masses (kDa) of the subunits are: 19.93 (RnfA), 17.69 (RnfB), 52.17 (RnfC), 39.16 (RnfD), 25.54 (RnfE), 24.86 (RnfG) and 9.63 (RnfH). The identities of bands corresponding to the subunits were confirmed by mass spectrometry. Purifications were performed more than five times with highly reproducible outcomes.

Source data

Extended Data Fig. 2 Data statistics and workflow for the cryo-EM data processing of RNF in DDM micelles of 6069 movies.

A) Representative micrograph and 2D class averages. B) Local resolution maps for different orientations of RNF. C) 2D distribution histogram of the viewing directions of particles used for the 3D reconstruction. D) Fourier shell correlation (FSC) curves. The gold-standard threshold of 0.143 was used to determine the overall resolution of the map. E) Workflow for data processing, leading NADH to a refined map at 3.11 Å resolution based on 94 K particles.

Extended Data Fig. 3 Data statistics and resolution for additional RNF data sets.

A) Sample as isolated with 2 mM NADH, with a 2D distribution histogram, FSC curve and local resolution maps for three different orientations. The gold-standard threshold of 0.143 was used to determine the overall resolution of the map. B) RNF reduced with 2 mM β-mercaptoethanol and 2 mM TCEP, with 2 mM of NADH added. C) RNF reduced with 5 mM sodium dithionite and 5 mM NADH. RnfG was sightly shifted towards RnfAE in this structure and less well ordered. In addition, the loop carrying the covalent FMND of RnfD was disordered and the cofactor was not defined in the map. D) RNF oxidized with 3 mM potassium ferricyanide. In this sample, the subunit RnfB was absent, although all data sets in this figure were collected from the same batch of RNF complex.

Extended Data Fig. 4 Details of the cryo-EM map for native A. vinelandii RNF.

A) Volume/multiple-contour rendering of the 3.11 Å resolution cryo-EM map in front, side, and top perspective, highlighting the DDM micelle and the flexibility of the long helix at the C-terminus of RnfC. B) The RnfD/RnfG region with the three membrane-embedded isoalloxazine cofactors, riboflavin (RBF) and a covalent FMN (FMND) in RnfD and a second covalent FMN in RnfG (FMNG). C) The RnfG subunit with the globular FMN-binding domain in the periplasm and the N-terminal stalk helix that anchors the subunit in the membrane.

Extended Data Fig. 5 Structure of RnfC and orthologous proteins.

Inset: Position of RnfC in the A. vinelandii RNF complex. RnfC comprises an N-terminal domain (blue) that is followed by a globular FMN-binding domain (white) with a non-covalently bound FMN cofactor. The two [4Fe:4S] clusters in RnfC are bound in the C-terminal-domain (red) and are in close distance allowing for efficient electron transfer (Fig. 2A). The peptide chain terminates in a long α-helix that is flexible (Extended Data Fig. 4A) and is in contact with RnfB and RnfH. Respiratory complex I binds NADH at the subunit NuoF, whose FMN-binding domain is functionally and structurally homologous to RnfC. The structure shows the E. coli protein (PDB 7AWT) with the FMN-binding domain in white. In NuoF, the C-terminal domain is not related to that of RnfC and only binds a single [4Fe:4S] cluster, N3. The extended C-terminus of NuoF is in contact with another subunit of the complex, NuoG. While NQR is a functional analog of respiratory complex I, its cytoplasmic subunit NqrA is not the binding site for NADH (PDB 8ACY). NqrA contains an N-terminal domain and a C-terminal one that terminates into a helix but does not bind any cofactors and has no known function in electron transfer within NQR.

Extended Data Fig. 6 Amino acid sequence alignments for RnfA and RnfE and architectural overlay.

A) The membrane subunits RnfA and RnfE align with a sequence identity of 24%, including the cysteine ligands to the [2Fe:2S] cluster FeS3. B) Architecture of the RnfAE heterodimer seen from the periplasmic side and along the pseudo-C2 axis, and detail of the cluster environment. C) Superposition of RnfA and RnfE that align with an overall r.m.s.d. of 1.3 Å for all atoms.

Extended Data Table 1 Bacterial strains, plasmids and primers used in this study
Extended Data Table 2 Cryo-EM data collection, refinement and validation statistics

Supplementary information

Reporting Summary

Supplementary Video 1

Concerted movement of the ‘switch module’ NqrCDE as a morph of the extreme conformations seen in cryo-EM (PDB 8A1T) and X-ray diffraction (PDB 8ACW).

Supplementary Video 2

Indications for the intrinsic dynamics of the RNF complex from AlphaFold2 models for the ortholog from R. capsulatus.

Source data

Source Data Extended Data Fig. 1

Unprocessed images of stained and UV-illuminated gels. The red boxes indicate the cutouts shown in Extended Data Fig. 1e.

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Zhang, L., Einsle, O. Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat Chem Biol (2024). https://doi.org/10.1038/s41589-024-01641-1

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