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Yorodumi- EMDB-26802: The CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacte... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26802 | |||||||||
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Title | The CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Full complex focused refinement of stalk | |||||||||
Map data | ||||||||||
Sample |
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Keywords | [NiFe] Hydrogenase / Membrane associated / Complex / Quinone Transport / ELECTRON TRANSPORT / OXIDOREDUCTASE (EC 1.12.99.6) / OXIDOREDUCTASE | |||||||||
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 MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Grinter R / Venugopal H / Kropp A / Greening C | |||||||||
Funding support | Australia, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26802.map.gz | 351.9 MB | EMDB map data format | |
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Header (meta data) | emd-26802-v30.xml emd-26802.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_26802.png | 61.5 KB | ||
Masks | emd_26802_msk_1.map | 729 MB | Mask map | |
Filedesc metadata | emd-26802.cif.gz | 6.8 KB | ||
Others | emd_26802_half_map_1.map.gz emd_26802_half_map_2.map.gz | 677.4 MB 677.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26802 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26802 | HTTPS FTP |
-Validation report
Summary document | emd_26802_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_26802_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_26802_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | emd_26802_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26802 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26802 | HTTPS FTP |
-Related structure data
Related structure data | 7uusMC 7utdC 7uurC 8dqvC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26802.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.5 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26802_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26802_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26802_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of the type 2 [NiFe]-hydrogenase Huc from Mycobacterium s...
Entire | Name: Complex of the type 2 [NiFe]-hydrogenase Huc from Mycobacterium smegmatis |
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Components |
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-Supramolecule #1: Complex of the type 2 [NiFe]-hydrogenase Huc from Mycobacterium s...
Supramolecule | Name: Complex of the type 2 [NiFe]-hydrogenase Huc from Mycobacterium smegmatis type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 833 KDa |
-Macromolecule #1: Hydrogenase-2, large subunit
Macromolecule | Name: Hydrogenase-2, large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: hydrogenase (acceptor) |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 57.447297 KDa |
Sequence | String: TELDLFVSPL GRVEGDLDVR VTINDGVVTS AWTEAAMFRG FEIILRGKDP QAGLIVCPRI CGICGGSHLY KSAYALDTAW RTHMPPNAT LIRNICQACE TLQSIPRYFY ALFAIDLTNK NYAKSKLYDE AVRRFAPYVG TSYQPGVVLS AKPVEVYAIF G GQWP(DHI)SSF ...String: TELDLFVSPL GRVEGDLDVR VTINDGVVTS AWTEAAMFRG FEIILRGKDP QAGLIVCPRI CGICGGSHLY KSAYALDTAW RTHMPPNAT LIRNICQACE TLQSIPRYFY ALFAIDLTNK NYAKSKLYDE AVRRFAPYVG TSYQPGVVLS AKPVEVYAIF G GQWP(DHI)SSF MVPGGVMSAP TLSDVTRAIA ILEHWNDNWL EKQWLGCSVD RWLENKTWND VLAWVDENES QYNSDCGF F IRYCLDVGLD KYGQGVGNYL ATGTYFEPSL YENPTIEGRN AALIGRSGVF ADGRYFEFDQ ANVTEDVTHS FYEGNRPLH PFEGETIPVN PEDGRRQGKY SWAKSPRYAV PGLGNVPLET GPLARRMAAS APDAETHQDD DPLFADIYNA IGPSVMVRQL ARMHEGPKY YKWVRQWLDD LELKESFYTK PVEYAEGKGF GSTEAARGAL SDWIVIEDSK IKNYQVVTPT AWNIGPRDAS E VLGPIEQA LVGSPIVDAE DPVELGHVAR SFDSCLVCTV H UniProtKB: Hydrogenase-2, large subunit |
-Macromolecule #2: Hydrogenase-2, small subunit
Macromolecule | Name: Hydrogenase-2, small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: hydrogenase (acceptor) |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 39.65977 KDa |
Sequence | String: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGGGGGENL YFQGSGGASV LWFQGGACSG NTMSFLNADE PNVVDLIVDF GLDLLWHPS LGLELGNNAQ KVFWDCAKGE RPLDIFVFEG TVIEAPNGTG QMDMFAGRPM KDWVTDLAGA AQIVVAIGDC A CFGGIPAM ...String: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGGGGGENL YFQGSGGASV LWFQGGACSG NTMSFLNADE PNVVDLIVDF GLDLLWHPS LGLELGNNAQ KVFWDCAKGE RPLDIFVFEG TVIEAPNGTG QMDMFAGRPM KDWVTDLAGA AQIVVAIGDC A CFGGIPAM EPNPSGSTGL QFHKREKGGF LGPDFRSKMG LPVINVPGCP AHPDWITQIL VALATGRAGD ITLDDLHRPE TF FKTFTQT GCTRVQFFEY KQSTLSFGEG TRTGCLFYEF GCRGPMTHSP CNRILWNRQS SKTRAGMPCL GCTEPEFPHF DLA PGTVFK TQKVSGMIPK EVPEGTDHLT YMGLAAAARI AAPQWSKEDM FVV UniProtKB: NADH ubiquinone oxidoreductase 20 kDa subunit |
-Macromolecule #3: [NiFe]-Hydrogenase Huc Membrane Associated Subunit
Macromolecule | Name: [NiFe]-Hydrogenase Huc Membrane Associated Subunit / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 19.275828 KDa |
Sequence | String: ASNGHSAGQN AIDELPDISP VDGIRRRLDD PQVAEALNSL LDHADLLAVL VKGLDGFVRR GDDIANNLTS AIGELKALNA ADTPIPALA ALKDVDLAGL ANSLATLSGG LVKATPALNA VLDSLTDQRG AEVLSALGDA LVAARTSAPP APRGVRGMWK T LRAAAKDP DVGRGVSYLI EVARVFGSKV UniProtKB: DUF1641 domain-containing protein |
-Macromolecule #4: NICKEL (III) ION
Macromolecule | Name: NICKEL (III) ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: 3NI |
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Molecular weight | Theoretical: 58.693 Da |
Chemical component information | ChemComp-3NI: |
-Macromolecule #5: CARBONMONOXIDE-(DICYANO) IRON
Macromolecule | Name: CARBONMONOXIDE-(DICYANO) IRON / type: ligand / ID: 5 / Number of copies: 8 / Formula: FCO |
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Molecular weight | Theoretical: 135.89 Da |
Chemical component information | ChemComp-FCO: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: MENAQUINONE-9
Macromolecule | Name: MENAQUINONE-9 / type: ligand / ID: 7 / Number of copies: 8 / Formula: MQ9 |
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Molecular weight | Theoretical: 785.233 Da |
Chemical component information | ChemComp-MQ9: |
-Macromolecule #8: FE3-S4 CLUSTER
Macromolecule | Name: FE3-S4 CLUSTER / type: ligand / ID: 8 / Number of copies: 24 / Formula: F3S |
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Molecular weight | Theoretical: 295.795 Da |
Chemical component information | ChemComp-F3S: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL | |||||||||
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Buffer | pH: 7.9 Component:
Details: pH 7.9 | |||||||||
Grid | Model: Quantifoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 9868 / Average exposure time: 4.0 sec. / Average electron dose: 60.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | PDB-7uus: |