+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22973 | |||||||||
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Title | Electron bifurcating flavoprotein Fix/EtfABCX | |||||||||
Map data | Electron bifurcating flavoprotein Fix/EtfABCX | |||||||||
Sample |
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Keywords | membrane-associated / flavin based electron bifurcation / FLAVOPROTEIN / FLAVOPROTEIN-Oxidoreductase complex | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With a quinone or similar compound as acceptor / iron-sulfur cluster binding / FAD binding / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima MSB8 (bacteria) / Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Feng X / Li H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Cryoelectron microscopy structure and mechanism of the membrane-associated electron-bifurcating flavoprotein Fix/EtfABCX. Authors: Xiang Feng / Gerrit J Schut / Gina L Lipscomb / Huilin Li / Michael W W Adams / Abstract: The electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX), also known as FixABCX for its role in nitrogen-fixing organisms, is a member of a family of electron-transferring ...The electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX), also known as FixABCX for its role in nitrogen-fixing organisms, is a member of a family of electron-transferring flavoproteins that catalyze electron bifurcation. EtfABCX enables endergonic reduction of ferredoxin (°' ∼-450 mV) using NADH (°' -320 mV) as the electron donor by coupling this reaction to the exergonic reduction of menaquinone (°' -80 mV). Here we report the 2.9 Å structure of EtfABCX, a membrane-associated flavin-based electron bifurcation (FBEB) complex, from a thermophilic bacterium. EtfABCX forms a superdimer with two membrane-associated EtfCs at the dimer interface that contain two bound menaquinones. The structure reveals that, in contrast to previous predictions, the low-potential electrons bifurcated from EtfAB are most likely directly transferred to ferredoxin, while high-potential electrons reduce the quinone via two [4Fe-4S] clusters in EtfX. Surprisingly, EtfX shares remarkable structural similarity with mammalian [4Fe-4S] cluster-containing ETF ubiquinone oxidoreductase (ETF-QO), suggesting an unexpected evolutionary link between bifurcating and nonbifurcating systems. Based on this structure and spectroscopic studies of a closely related EtfABCX, we propose a detailed mechanism of the catalytic cycle and the accompanying structural changes in this membrane-associated FBEB system. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22973.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-22973-v30.xml emd-22973.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22973_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22973.png | 61.8 KB | ||
Masks | emd_22973_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-22973.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22973 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22973 | HTTPS FTP |
-Validation report
Summary document | emd_22973_validation.pdf.gz | 410.2 KB | Display | EMDB validaton report |
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Full document | emd_22973_full_validation.pdf.gz | 409.8 KB | Display | |
Data in XML | emd_22973_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_22973_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22973 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22973 | HTTPS FTP |
-Related structure data
Related structure data | 7koeMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22973.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Electron bifurcating flavoprotein Fix/EtfABCX | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22973_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
Entire | Name: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX |
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Components |
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-Supramolecule #1: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
Supramolecule | Name: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Thermotoga maritima MSB8 (bacteria) |
-Macromolecule #1: Electron transfer flavoprotein, beta subunit
Macromolecule | Name: Electron transfer flavoprotein, beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 33.003957 KDa |
Recombinant expression | Organism: Pyrococcus furiosus COM1 (archaea) |
Sequence | String: MAHHHHHHHH HANVVVCIKQ VPDTTNVRID RKTNNLVREG VPSIINPDDE RALELASQLK EKFGATVYVI TMGPPQAKEA LKDAIAFGL DEAVHLSDRT FAGADTLATT YTLYWGIKKI EERIGKIDLI LTGKQAVDGD TGQVGPGLAT RFGYALGAYV V RIEEIDPE ...String: MAHHHHHHHH HANVVVCIKQ VPDTTNVRID RKTNNLVREG VPSIINPDDE RALELASQLK EKFGATVYVI TMGPPQAKEA LKDAIAFGL DEAVHLSDRT FAGADTLATT YTLYWGIKKI EERIGKIDLI LTGKQAVDGD TGQVGPGLAT RFGYALGAYV V RIEEIDPE KKEMVIVRRL DQGFEKIRLK LPAVLTITDE LNKPRYADLP NLIRAIRYEP IVWTHKDLGL DPKKCGFFGS PT RVVSTNI PPARKGGDII SKNEDPEVAA EKLIEALKKF EAVRLVEALK PVLEGEKDE UniProtKB: Electron transfer flavoprotein, beta subunit |
-Macromolecule #2: Electron transfer flavoprotein, alpha subunit
Macromolecule | Name: Electron transfer flavoprotein, alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 36.801758 KDa |
Recombinant expression | Organism: Pyrococcus furiosus COM1 (archaea) |
Sequence | String: MSEKKIIFVL IEHHGGKAHP VSWELIGKAR DLASKLENSE VWGVLLGEGL ESVAKEAIQR GADKVLYVKN REFNTYVNYL YKKALVDMV RKYRPEIFLI GATLEGRELA GMVATELETG LTADCTGLDI IPDKKLLAMT RPTFGGNLMA TIMCPDHRPQ M ATVRPGVM ...String: MSEKKIIFVL IEHHGGKAHP VSWELIGKAR DLASKLENSE VWGVLLGEGL ESVAKEAIQR GADKVLYVKN REFNTYVNYL YKKALVDMV RKYRPEIFLI GATLEGRELA GMVATELETG LTADCTGLDI IPDKKLLAMT RPTFGGNLMA TIMCPDHRPQ M ATVRPGVM KELPPDPERT GEIIEEEYDL GTFDKLIEIL ETIPLQTQVN LEYAPVVVAG GKGVGGPEGF KKLKELADLL GG EVGASRA AVKAGWISPE HQVGQTGKTV RPVLYFACGI SGAIQHVVGI KESEIIVAIN IDEKAPIFDI ADIGIVGDLH KVV PALTAK LRELLNKSGV KK UniProtKB: Electron transfer flavoprotein, alpha subunit |
-Macromolecule #3: Electron transfer flavoprotein-quinone oxidoreductase FixC
Macromolecule | Name: Electron transfer flavoprotein-quinone oxidoreductase FixC type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO EC number: Oxidoreductases; Acting on the CH-NH group of donors; With a quinone or similar compound as acceptor |
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Source (natural) | Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 49.040773 KDa |
Recombinant expression | Organism: Pyrococcus furiosus COM1 (archaea) |
Sequence | String: MKIEFDVVVV GAGPSGLSCA YVLAKNGLKV AVVEKGEYPG SKNVMGGVLY VHPLKEIMPD FLEKAANSKA LERNVIEQNL WLLGNEGVI KIGHRNVEWK ENPNAFTVLR ANFDRWFAQE VEKAGALIIP KTKVEDFLRN EKGEIAGVVT SRPKGEIHSK A VVIAEGVN ...String: MKIEFDVVVV GAGPSGLSCA YVLAKNGLKV AVVEKGEYPG SKNVMGGVLY VHPLKEIMPD FLEKAANSKA LERNVIEQNL WLLGNEGVI KIGHRNVEWK ENPNAFTVLR ANFDRWFAQE VEKAGALIIP KTKVEDFLRN EKGEIAGVVT SRPKGEIHSK A VVIAEGVN PILTMKAGLR KEDLKPHMVA VAVKEVISVP EDVVNRVFGV EGNDGATIEL LGSWSEGMFG MGFLYANRSS VS LGCGVLL EDLRKKKIKP YQLLENLKNH PVISDMLGEY RNNTMEYLAH LIPEGGYYAM PKVYGDRVLV CGDAAMLVNS IHR EGSNHA ITSGRLAAET LLEAFEKGDF SEKILKNYYL RLKESFILKD LEKYKDLMPT MEKNHQFVEI YPDLANDALK RFLQ VDGTP KWDVQKQIAD MVLSRRSLIG ISLDLLRFWR AVR UniProtKB: Putative electron transfer flavoprotein-quinone oxidoreductase FixC |
-Macromolecule #4: Ferredoxin-like protein
Macromolecule | Name: Ferredoxin-like protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 10.73022 KDa |
Recombinant expression | Organism: Pyrococcus furiosus COM1 (archaea) |
Sequence | String: MRIEDKLYLN RYRTDEENPH LKIKDESICA EKCSDRPCVS CCPADVYEWT ESGMEVKFEG CLECGTCRIV CPFGNIEWNY PRGNYGVLY KFG UniProtKB: Ferredoxin-like protein |
-Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 6 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #6: MENAQUINONE-7
Macromolecule | Name: MENAQUINONE-7 / type: ligand / ID: 6 / Number of copies: 2 / Formula: MQ7 |
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Molecular weight | Theoretical: 648.999 Da |
Chemical component information | ChemComp-MQ7: |
-Macromolecule #7: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 4 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 9096 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7koe: |