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Yorodumi- EMDB-26767: The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26767 | |||||||||
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Title | The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) / Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.19 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_26767.map.gz | 88.8 MB | EMDB map data format | |
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Header (meta data) | emd-26767-v30.xml emd-26767.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26767_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_26767.png | 209.2 KB | ||
Others | emd_26767_half_map_1.map.gz emd_26767_half_map_2.map.gz | 164.8 MB 164.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26767 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26767 | HTTPS FTP |
-Validation report
Summary document | emd_26767_validation.pdf.gz | 883.3 KB | Display | EMDB validaton report |
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Full document | emd_26767_full_validation.pdf.gz | 882.9 KB | Display | |
Data in XML | emd_26767_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_26767_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26767 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26767 | HTTPS FTP |
-Related structure data
Related structure data | 7utdMC 7uurC 7uusC 8dqvC M: atomic model generated by this map C: citing same article (ref.) |
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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_26767.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_26767_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26767_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 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: MC2 155 |
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: 57.217078 KDa |
Sequence | String: LDLFVSPLGR VEGDLDVRVT INDGVVTSAW TEAAMFRGFE IILRGKDPQA GLIVCPRICG ICGGSHLYKS AYALDTAWRT HMPPNATLI RNICQACETL QSIPRYFYAL FAIDLTNKNY AKSKLYDEAV RRFAPYVGTS YQPGVVLSAK PVEVYAIFGG Q WP(DHI)SSFMV ...String: LDLFVSPLGR VEGDLDVRVT INDGVVTSAW TEAAMFRGFE IILRGKDPQA GLIVCPRICG ICGGSHLYKS AYALDTAWRT HMPPNATLI RNICQACETL QSIPRYFYAL FAIDLTNKNY AKSKLYDEAV RRFAPYVGTS YQPGVVLSAK PVEVYAIFGG Q WP(DHI)SSFMV PGGVMSAPTL SDVTRAIAIL EHWNDNWLEK QWLGCSVDRW LENKTWNDVL AWVDENESQY NSDCGFFI R YCLDVGLDKY GQGVGNYLAT GTYFEPSLYE NPTIEGRNAA LIGRSGVFAD GRYFEFDQAN VTEDVTHSFY EGNRPLHPF EGETIPVNPE DGRRQGKYSW AKSPRYAVPG LGNVPLETGP LARRMAASAP DAETHQDDDP LFADIYNAIG PSVMVRQLAR MHEGPKYYK WVRQWLDDLE LKESFYTKPV EYAEGKGFGS TEAARGALSD WIVIEDSKIK NYQVVTPTAW NIGPRDASEV L GPIEQALV GSPIVDAEDP VELGHVARSF DSCLVCTVH |
-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: ATCC 700084 / mc(2)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 |
-Macromolecule #3: Type 2 [NiFe]-hydrogenase Huc membrane adapter subunit
Macromolecule | Name: Type 2 [NiFe]-hydrogenase Huc membrane adapter 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: 6.416264 KDa |
Sequence | String: SPVDGIRRRL DDPQVAEALN SLLDHADLLA VLVKGLDGFV RRGDDIANNL TSAIGELKAL |
-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: 3113 / Average exposure time: 6.0 sec. / Average electron dose: 66.0 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 | 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 / Target criteria: Correlation coefficient |
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Output model | PDB-7utd: |