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Yorodumi- EMDB-2513: Electron cryo-microscopy of F420-reducing [NiFe] hydrogenase Frh -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2513 | |||||||||
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Title | Electron cryo-microscopy of F420-reducing [NiFe] hydrogenase Frh | |||||||||
Map data | FrhABG dodecamer | |||||||||
Sample |
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Keywords | hydrogenase / flavoprotein / [NiFe] hydrogenase / electron transfer / ferredoxin | |||||||||
Function / homology | Function and homology information 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 | Methanothermobacter marburgensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Allegretti M / Mills DJ / McMullan G / Kuehlbrandt W / Vonck J | |||||||||
Citation | Journal: Elife / Year: 2014 Title: Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. Authors: Matteo Allegretti / Deryck J Mills / Greg McMullan / Werner Kühlbrandt / Janet Vonck / Abstract: The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct ...The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2513.map.gz | 39.8 MB | EMDB map data format | |
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Header (meta data) | emd-2513-v30.xml emd-2513.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_2513.tif | 765.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2513 | HTTPS FTP |
-Validation report
Summary document | emd_2513_validation.pdf.gz | 326.4 KB | Display | EMDB validaton report |
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Full document | emd_2513_full_validation.pdf.gz | 325.6 KB | Display | |
Data in XML | emd_2513_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2513 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2513 | HTTPS FTP |
-Related structure data
Related structure data | 4ci0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2513.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | FrhABG dodecamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : F420 reducing hydrogenase
Entire | Name: F420 reducing hydrogenase |
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Components |
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-Supramolecule #1000: F420 reducing hydrogenase
Supramolecule | Name: F420 reducing hydrogenase / type: sample / ID: 1000 Oligomeric state: a dodecamer of the heterotrimer FrhA, FrhB, FrhG Number unique components: 3 |
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Molecular weight | Experimental: 1.2 MDa / Theoretical: 1.2 MDa |
-Macromolecule #1: F420-reducing hydrogenase, subunit alpha
Macromolecule | Name: F420-reducing hydrogenase, subunit alpha / type: protein_or_peptide / ID: 1 / Name.synonym: FrhA / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No |
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Source (natural) | Organism: Methanothermobacter marburgensis (archaea) / Strain: DSM 2133 / Location in cell: cytoplasm |
Molecular weight | Experimental: 440 KDa / Theoretical: 440 KDa |
Sequence | UniProtKB: coenzyme F420 hydrogenase subunit alpha InterPro: Coenzyme F420 hydrogenase, subunit alpha, Coenzyme F420 hydrogenase subunit beta, archaea, Coenzyme F420 hydrogenase, subunit gamma |
-Macromolecule #2: F420-reducing hydrogenase, subunit beta
Macromolecule | Name: F420-reducing hydrogenase, subunit beta / type: protein_or_peptide / ID: 2 / Name.synonym: FrhB / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No |
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Source (natural) | Organism: Methanothermobacter marburgensis (archaea) / Strain: DSM 2133 / Location in cell: cytoplasm |
Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa |
Sequence | UniProtKB: coenzyme F420 hydrogenase subunit beta InterPro: Coenzyme F420 hydrogenase, subunit alpha, Coenzyme F420 hydrogenase subunit beta, archaea, Coenzyme F420 hydrogenase, subunit gamma |
-Macromolecule #3: F420-reducing hydrogenase, subunit gamma
Macromolecule | Name: F420-reducing hydrogenase, subunit gamma / type: protein_or_peptide / ID: 3 / Name.synonym: FrhG / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No |
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Source (natural) | Organism: Methanothermobacter marburgensis (archaea) / Strain: DSM 2133 / Location in cell: cytoplasm |
Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa |
Sequence | UniProtKB: coenzyme F420 hydrogenase subunit beta 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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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 |
Details | data was collected in movie mode |
Date | May 27, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 235 / Average electron dose: 22 e/Å2 Details: Every image is the average of six frames recorded by the direct electron detector aligned to each other Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 106000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
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Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 26000 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: Coot |
Details | The structure was built using Coot based on an earlier model built into a lower resolution EM map |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-4ci0: |