De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy
- Max Planck Institute of Biophysics, Germany
- Max Planck Institute for Terrestrial Microbiology, Germany
- Japan Science and Technology Agency, Japan
Figures
Figure 1
Cryo-electron microscopy and image processing.
(A) A representative area of an electron micrograph taken at 200 kV on an FEI Polara. The defocus was determined as 2.05 µm. The scale bar represents 25 nm. (B) Representative class averages and …
Figure 2
High-resolution cryo-EM map of Frh.
(A) view down the twofold axis. Each of the 12 FrhABG heterotrimers is shown in a different color. (B) The same view as (A) with the two trimers at the front removed, (C) view down the threefold …
Figure 3
Sequence and secondary structure of FrhA and a comparison with homologous proteins.
(A) Alignment of the [NiFe]-hydrogenase large subunit from Desulfovibrio vulgaris Hildenborough (first line) with Methanothermobacter marburgensis FrhA (third line). The second line shows the …
Figure 4
Models of Frh subunits.
(A) FrhA, (B) FrhG, and (C) FrhB in rainbow colors from blue (N-terminus) to red (C-terminus). (D) Stereo pair of the FrhABG heterotrimer with the string of four bound Fe-S clusters (orange/yellow), …
Figure 5
Details of the model and map.
(A) The ferredoxin domain of FrhG. The eight cysteine residues surrounding the two [Fe4S4] clusters are shown in green. (B) β-Sheet in FrhB. The strands are clearly separated. (C) The dimer …
Figure 6
Sequence and secondary structure of FrhG and a comparison with homologous proteins.
(A) Alignment of the [NiFe]-hydrogenase small subunit from Desulfovibrio vulgaris Hildenborough (first line) with Methanothermobacter marburgensis FrhG (third line) and ferredoxin from Peptostreptoco…
Figure 7
Sequence and secondary structure of FrhB.
Light gray font: No density; green highlight: α-helix; gray highlight: β-strand. Second line: Consensus sequence of FrhB species. Capitals: conserved residues; lower case: similar residues (h: …
Figure 8
Electron-transfer chain and F420.
Maps in the absence (A) and presence (B) of the substrate F420 differ in a region near a conserved loop between two β-strands near the FAD (carbons in yellow). The isoalloxazine ring of F420 fitted …
Figure 9
Alignment of the FrhB family of F420-binding proteins.
FrhB: FrhB of Methanothermobacter marburgensis DSM 2133; GS: F420-dependent glutamate synthase from M. marburgensis, ADL58239; FqoF: F420H2:quinone oxidoreductase subunit F from Archaeoglobus …
Figure 10
Resolution estimations and B-factor determination.
(A) Fourier shell correlation plot, showing the resolution for the substrate-free map (black) and the F420-containing map (red). At the 0.5 FSC criterion, the resolution is 3.9 and 4.0 Å, …
Figure 11
Model of the dodecameric Frh complex.
Each FrhABG heterotrimer is colored differently with the same color scheme as the map in Figure 1. (A) View down the twofold axis, (B) view of the FrhB trimer, and (C) view of the closely packed …
Figure 12
A comparison of (A) Frh and (B) the group I [NiFe] hydrogenase from Desulfovibrio gigas (2wpn) (Marques et al., 2010) shows a lower intersubunit contact area in the former. The large subunit/FrhA is …
Videos
Video 1
The Frh map at different density levels.
The Frh map contains high densities corresponding to the metal clusters. The map, filtered to 5.5 Å for clarity, is shown at increasing isosurface levels. At density level 1 (gray), the whole …
Video 2
FrhA.
The model of FrhA is shown superimposed on the map.
Video 3
FrhG.
The model of FrhG is shown superimposed on the map.
Video 4
FrhB.
The model of FrhB is shown superimposed on the map.
Video 5
Conserved residues in FrhB.
The FrhB model is shown with conserved residues in red, similar residues in orange and unconserved residues in gray (see Figure 7 for sequence). FAD is yellow and F420 green. Highly conserved …
Video 6
The Frh dodecamer.
A model of the tetrameric Frh complex.
