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- EMDB-2096: Cryo-EM structure of the F420-reducing [NiFe]-hydrogenase from a ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2096 | |||||||||
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Title | Cryo-EM structure of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon at near-atomic resolution | |||||||||
![]() | reconstruction of Frh complex | |||||||||
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![]() | hydrogenase / [NiFe] hydrogenase / methanogenesis / F420-reducing hydrogenase | |||||||||
Function / homology | ![]() coenzyme F420 hydrogenase / coenzyme F420 hydrogenase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Mills DJ / Vitt S / Strauss M / Shima S / Vonck J | |||||||||
![]() | ![]() Title: De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. Authors: Deryck J Mills / Stella Vitt / Mike Strauss / Seigo Shima / Janet Vonck / ![]() Abstract: Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the ...Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI:http://dx.doi.org/10.7554/eLife.00218.001. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 84.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 122.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zfsMC ![]() 2097C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | reconstruction of Frh complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : F420-reducing [NiFe] hydrogenase Frh
Entire | Name: F420-reducing [NiFe] hydrogenase Frh |
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Components |
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-Supramolecule #1000: F420-reducing [NiFe] hydrogenase Frh
Supramolecule | Name: F420-reducing [NiFe] hydrogenase Frh / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1 |
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Molecular weight | Experimental: 1.2 MDa / Theoretical: 1.2 MDa |
-Macromolecule #1: F420-reducing [NiFe] hydrogenase
Macromolecule | Name: F420-reducing [NiFe] hydrogenase / type: protein_or_peptide / ID: 1 / Name.synonym: Frh, FrhABG Details: The Frh complex is a tetrahedral dodecamer of an FrhA, FrhB, FrhG heterotrimer Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 1.2 MDa / Theoretical: 1.2 MDa |
Sequence | InterPro: Coenzyme F420 hydrogenase, subunit alpha, Coenzyme F420 hydrogenase subunit beta, archaea, Coenzyme F420 hydrogenase, subunit gamma |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.6 / Details: 50mM Tris-HCl, 0.025mM FAD |
Grid | Details: freshly glow discharged Quantifoil holey grid (1 micrometer holes) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 103 K / Instrument: FEI VITROBOT MARK I / Method: blotting 2.5 seconds before plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 77 K / Max: 80 K / Average: 79 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification |
Date | Aug 26, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 101 / Average electron dose: 15 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 61400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 1.69 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | EMAN2 |
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CTF correction | Details: each micrograph |
Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 84000 |
Final two d classification | Number classes: 2134 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: chimera, coot |
Details | Protocol: A rigid body fit was done in Chimera and the model manually rebuilt in Coot. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3zfs: |