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Yorodumi- PDB-8dqv: The 1.52 angstrom CryoEM structure of the [NiFe]-hydrogenase Huc ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dqv | |||||||||
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Title | The 1.52 angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L) | |||||||||
Components | (Hydrogenase-2, ...) x 2 | |||||||||
Keywords | ELECTRON TRANSPORT / [NiFe] Hydrogenase / Membrane-associated / Complex / Quinone Transport | |||||||||
Function / homology | Function and homology information hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.52 Å | |||||||||
Authors | Grinter, R. / Venugopal, H. / Kropp, A. / Greening, C. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis for bacterial energy extraction from atmospheric hydrogen. Authors: Rhys Grinter / Ashleigh Kropp / Hari Venugopal / Moritz Senger / Jack Badley / Princess R Cabotaje / Ruyu Jia / Zehui Duan / Ping Huang / Sven T Stripp / Christopher K Barlow / Matthew ...Authors: Rhys Grinter / Ashleigh Kropp / Hari Venugopal / Moritz Senger / Jack Badley / Princess R Cabotaje / Ruyu Jia / Zehui Duan / Ping Huang / Sven T Stripp / Christopher K Barlow / Matthew Belousoff / Hannah S Shafaat / Gregory M Cook / Ralf B Schittenhelm / Kylie A Vincent / Syma Khalid / Gustav Berggren / Chris Greening / Abstract: Diverse aerobic bacteria use atmospheric H as an energy source for growth and survival. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and ...Diverse aerobic bacteria use atmospheric H as an energy source for growth and survival. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments. Atmospheric H oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H amid ambient levels of the catalytic poison O and how the derived electrons are transferred to the respiratory chain. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H at the expense of O, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H in ambient air. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqv.cif.gz | 548 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqv.ent.gz | 456.1 KB | Display | PDB format |
PDBx/mmJSON format | 8dqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dqv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8dqv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8dqv_validation.xml.gz | 66.5 KB | Display | |
Data in CIF | 8dqv_validation.cif.gz | 103.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqv ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqv | HTTPS FTP |
-Related structure data
Related structure data | 27661MC 7utdC 7uurC 7uusC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Hydrogenase-2, ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 57217.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QUM7, hydrogenase (acceptor) #2: Protein | Mass: 35071.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7G634, hydrogenase (acceptor) |
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-Non-polymers , 7 types, 612 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-F3S / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of the type 2 [NiFe]-hydrogenase Huc from Mycobacterium smegmatis Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.833 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: MC2 155 | |||||||||||||||
Buffer solution | pH: 7.9 / Details: pH 7.9 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid type: Quantifoil | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: HELIUM / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 60.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9868 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3800000 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153359 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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