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Open data
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Basic information
Entry | Database: PDB / ID: 4ci0 | ||||||
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Title | Electron cryo-microscopy of F420-reducing NiFe hydrogenase Frh | ||||||
![]() | (F420-REDUCING HYDROGENASE, SUBUNIT ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / ELECTRON TRANSFER / FERREDOXIN | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
![]() | Allegretti, M. / Mills, D.J. / McMullan, G. / Kuehlbrandt, W. / Vonck, J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.3 KB | Display | ![]() |
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PDB format | ![]() | 136.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2513MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: T (tetrahedral)) |
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Components
-F420-REDUCING HYDROGENASE, SUBUNIT ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 42696.773 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-386 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: D9PYF9, coenzyme F420 hydrogenase |
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#2: Protein | Mass: 30267.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: D9PYF7, coenzyme F420 hydrogenase |
#3: Protein | Mass: 30778.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: D9PYF6, coenzyme F420 hydrogenase |
-Non-polymers , 6 types, 9 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FAD.gif)
#4: Chemical | ChemComp-FE / | ||||
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#5: Chemical | ChemComp-NI / | ||||
#6: Chemical | ChemComp-FE2 / | ||||
#7: Chemical | ChemComp-SF4 / #8: Chemical | ChemComp-ZN / | #9: Chemical | ChemComp-FAD / | |
-Details
Nonpolymer details | ZINC ION (ZN): A ZINC ION IS SHARED BY TWO FRHG SUBUNITS |
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Sequence details | THE SEQUENCE AFTER HIS386 HAS BEEN REMOVED BY AN ENDOPEPTID |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: F420 REDUCING HYDROGENASE / Type: COMPLEX |
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Buffer solution | Name: 50MM TRIS-HCL, 0.025MM FAD / pH: 7.6 / Details: 50MM TRIS-HCL, 0.025MM FAD |
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 103, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOTTING 2.5 SECONDS BEFORE PLUNGING, |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: May 27, 2013 / Details: DATA WAS COLLECTED IN MOVIE MODE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 106000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.2 mm |
Specimen holder | Temperature: 79 K |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 235 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: EACH IMAGE | ||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||
3D reconstruction | Method: MAXIMUM LIKELIHOOD / Resolution: 3.36 Å / Num. of particles: 26000 / Nominal pixel size: 1.32 Å / Actual pixel size: 1.32 Å / Magnification calibration: FIT TO ATOMIC MODEL Details: FRH IS A FRHABG DODECAMER WITH TETRAHEDRAL SYMMETRY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2513. (DEPOSITION ID: 12073). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--CRYO-EM | ||||||||||||
Atomic model building | PDB-ID: 3ZFS | ||||||||||||
Refinement | Highest resolution: 3.36 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.36 Å
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