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Yorodumi- EMDB-16879: Cryo-EM structure of the electron bifurcating transhydrogenase St... -
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Entry | Database: EMDB / ID: EMD-16879 | |||||||||
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Title | Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 1) | |||||||||
Map data | Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata in the apo state | |||||||||
Sample |
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Keywords | flavin based Electron-bifurcation / transhydrogenases / anaerobic metabolism / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information hydrogen dehydrogenase / hydrogen dehydrogenase activity / formate dehydrogenase / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Sporomusa ovata DSM 2662 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kumar A / Kremp F / Mueller V / Schuller JM | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular architecture and electron transfer pathway of the Stn family transhydrogenase. Authors: Anuj Kumar / Florian Kremp / Jennifer Roth / Sven A Freibert / Volker Müller / Jan M Schuller / Abstract: The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood- ...The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16879.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-16879-v30.xml emd-16879.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_16879.png | 127 KB | ||
Others | emd_16879_half_map_1.map.gz emd_16879_half_map_2.map.gz | 94.8 MB 94.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16879 | HTTPS FTP |
-Related structure data
Related structure data | 8oh9MC 8oh5C 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_16879.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata in the apo state | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_16879_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16879_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the electron bifurcating trans-hydrogenase S...
Entire | Name: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata in the oxidised state |
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Components |
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-Supramolecule #1: Cryo-EM structure of the electron bifurcating trans-hydrogenase S...
Supramolecule | Name: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata in the oxidised state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Sporomusa ovata DSM 2662 (bacteria) |
Molecular weight | Theoretical: 850 KDa |
-Macromolecule #1: NAD-dependent formate dehydrogenase gamma subunit
Macromolecule | Name: NAD-dependent formate dehydrogenase gamma subunit / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Sporomusa ovata DSM 2662 (bacteria) |
Molecular weight | Theoretical: 18.973877 KDa |
Sequence | String: MCNSCEKELE TKFPADKIDL TLLEPVFKEY AGKAGSIIGI LQKTQEIYGY LPLAALQAIA DNTDNKRAKI YGIATFYSQF RLNPVGKYV ILQCQGTACH VLGSKAIGSA ICDELGITPG QTTADGLFTL EDVACLGCCS LAPVIMINGE AYGKLTPTSV R KILQDIAE AEKGGVVSEG UniProtKB: NAD-dependent formate dehydrogenase gamma subunit |
-Macromolecule #2: NAD-reducing hydrogenase subunit HoxF
Macromolecule | Name: NAD-reducing hydrogenase subunit HoxF / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Sporomusa ovata DSM 2662 (bacteria) |
Molecular weight | Theoretical: 63.569254 KDa |
Sequence | String: MKVRVGLGSC GIAAGGRKVM DRLAQEIKNH GKEIELLPTG CIGMCFYEPI VDVFDGDKVY SYANVTADMA TEIFNSHIIG GQPLTQYIV STTEKPYTIL AKQVRIALRN CGVIDPENVD EYKANDGYKA LSKALKEMTP EEVIEEIKVA GLRGRGGAGF P TWFKWNAA ...String: MKVRVGLGSC GIAAGGRKVM DRLAQEIKNH GKEIELLPTG CIGMCFYEPI VDVFDGDKVY SYANVTADMA TEIFNSHIIG GQPLTQYIV STTEKPYTIL AKQVRIALRN CGVIDPENVD EYKANDGYKA LSKALKEMTP EEVIEEIKVA GLRGRGGAGF P TWFKWNAA RQSKGEIKYV VCNADEGDPG AFMDRSVLEG DPHALLEGMA ICGYAIGANE GHIYCRAEYP LAIKRLEIAI AD AKQRNLL GKNIMGTNFS FDMKIKKGAG AFVCGEETAL IASLEGERGM PRLKPPFPAQ SGFWGKPTNI NNVETFANVP WIM YNGGSA YAAYGTEKSK GTKVFALAGK IKNGGLVEVP MGMSLREVIY DIGGGILNDR EFKAVQMGGP SGGCIPKQLL DTPV DYDSI NKTGAIMGSG GMIVMDETTC MVDMARFFLD FTVKESCGKC IYCRIGTKRM LEILERITTG EGREGDIEEL EELSI SIKD GSLCGLGQTA PNPVLTTIRY FRDEYEAHIR DKKCPAKSCK PLLTYTINQD NCKGCTLCAQ KCPVQAITGE KKKPHV IDQ ALCTKCGNCA SVCRLDAVCI E UniProtKB: NAD-reducing hydrogenase subunit HoxF |
-Macromolecule #3: Formate dehydrogenase-O, major subunit
Macromolecule | Name: Formate dehydrogenase-O, major subunit / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Sporomusa ovata DSM 2662 (bacteria) |
Molecular weight | Theoretical: 126.488734 KDa |
Sequence | String: MSKISINING RELVVSAGQT ILQAAAEHGI EIPHLCHDER IQPYGACGLC VVEVEGSPKL VRSCATSVQN GQVIRTDTSR TVVARKTAL QLLASDHRGD CRPPCMLACP AQTDCQGYVG LIANGQYEEA LKLIKDKMPI PASIGKICPH PCETACRREL V EEPISIAQ ...String: MSKISINING RELVVSAGQT ILQAAAEHGI EIPHLCHDER IQPYGACGLC VVEVEGSPKL VRSCATSVQN GQVIRTDTSR TVVARKTAL QLLASDHRGD CRPPCMLACP AQTDCQGYVG LIANGQYEEA LKLIKDKMPI PASIGKICPH PCETACRREL V EEPISIAQ LKSFVAEVDL NGNQYQPPMK PATGKKVAVV GAGPAGLTAA YFLARDGHKV VIYEAMPHPG GMLRYGIPQY RL DKALLDA EVALMTKMGI EIIYNTKIGD DVSLDYLHDN YDAVFLGIGS WQSQGLRCKG EDMEGVLGGI DFLREVTMNS NIT LGGKVL VVGGGNTAMD VARTSKRLGA EEVTIIYRRT IDEMPAEKIE IHEAQEEGVK FQLLVAPVEV LGENGHAKAL KCEI MRLGE PDASGRRKPE PTGETVVYEA DRIIAAIGQK TVIGNIKDIA TDKSGNIIVN GGAFTTNRDK VFAGGDAVTG PKIAI DAIA QGKNAAQVID SYLNGCLVPH ADSQYFTQKD ITAADLADRA KAPRVSLTVE DAEVRNKSFM QVAKTFTEEE ALRESK RCL ECGCRDYFEC QLIKYIQDYD VSTEKDSQVE CHKTTEFDNH PFIERNPDKC VLCGLCVRVC DEVVGATAIG LVGRGFD SV IMPEFKLPLS ETACISCGQC VDVCPTGACM EKQVSYKQIP ANMDSMASVC GYCGVGCNVN IEYKGDVVFR VTPDRVND D GWLCQRGKFG LGHANDKARL TAPVIKRNGQ FVKVDWNEAN LEVVKRLQAV VAAYGKDSIG VVVSPRLTNE ELFLAGKLA DAVNTTIKTS YSVDGGSGLG SVLGYDASTN SFAELDNSDF VLTLGKVKEN HPVLDFKIRL SGVCSVAWPQ SLANTADMKV FLKALLNLG VDENKVAEKT EGFAELKASL ADVKVSEEIQ ALAQKYAKAA KPLIVIDEDT VSAEAVKLMA YAAVITGKIG A AYRGIILV RTKNNTQGAV DMGFVMPVSA VAQGIESGKI KALVVIGEDP AAYPQESALL QKLSFLVVYD MFMTKTATAA DM VVPLVSS AEVNGTYTRS DRRIQAVRAA IQPKTGKATL QILIETLKSL GIKYDTIADV RAAIASEVSN YAGMDAADFG TTV YWPNNK NVLYTDGFAT EGQKAILAAV GDVPVFVEKK KYDSVEMNFV NGRQSL UniProtKB: Formate dehydrogenase-O, major subunit |
-Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 12 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 36 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #7: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 4 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116573 |