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- EMDB-22973: Electron bifurcating flavoprotein Fix/EtfABCX -

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Basic information

Entry
Database: EMDB / ID: EMD-22973
TitleElectron bifurcating flavoprotein Fix/EtfABCX
Map dataElectron bifurcating flavoprotein Fix/EtfABCX
Sample
  • Complex: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
    • Protein or peptide: Electron transfer flavoprotein, beta subunit
    • Protein or peptide: Electron transfer flavoprotein, alpha subunit
    • Protein or peptide: Electron transfer flavoprotein-quinone oxidoreductase FixC
    • Protein or peptide: Ferredoxin-like protein
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MENAQUINONE-7
  • Ligand: IRON/SULFUR CLUSTER
Keywordsmembrane-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 / oxidoreductase activity / electron transfer activity / iron ion binding
Similarity search - Function
Ferredoxin-like, FixX / Protein FixC-like / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain ...Ferredoxin-like, FixX / Protein FixC-like / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / FAD-binding domain / FAD binding domain / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Rossmann-like alpha/beta/alpha sandwich fold / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Electron transfer flavoprotein, beta subunit / Ferredoxin-like protein / Putative electron transfer flavoprotein-quinone oxidoreductase FixC / Electron transfer flavoprotein, alpha subunit
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria) / Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeng X / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: 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
DepositionNov 8, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7koe
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22973.png

Downloads & links

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Map

FileDownload / File: emd_22973.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron bifurcating flavoprotein Fix/EtfABCX
Voxel sizeX=Y=Z: 1.029 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.022
Minimum - Maximum-0.15086962 - 0.26641878
Average (Standard dev.)0.00009795881 (±0.0038971945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.28003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.280329.280329.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1510.2660.000

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Supplemental data

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Mask #1

Fileemd_22973_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : octameric complex of electron bifurcating flavoprotein Fix/EtfABCX

EntireName: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
Components
  • Complex: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
    • Protein or peptide: Electron transfer flavoprotein, beta subunit
    • Protein or peptide: Electron transfer flavoprotein, alpha subunit
    • Protein or peptide: Electron transfer flavoprotein-quinone oxidoreductase FixC
    • Protein or peptide: Ferredoxin-like protein
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MENAQUINONE-7
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX

SupramoleculeName: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)

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Macromolecule #1: Electron transfer flavoprotein, beta subunit

MacromoleculeName: Electron transfer flavoprotein, beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 33.003957 KDa
Recombinant expressionOrganism: Pyrococcus furiosus COM1 (archaea)
SequenceString: 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

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Macromolecule #2: Electron transfer flavoprotein, alpha subunit

MacromoleculeName: Electron transfer flavoprotein, alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 36.801758 KDa
Recombinant expressionOrganism: Pyrococcus furiosus COM1 (archaea)
SequenceString: 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

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Macromolecule #3: Electron transfer flavoprotein-quinone oxidoreductase FixC

MacromoleculeName: 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
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 49.040773 KDa
Recombinant expressionOrganism: Pyrococcus furiosus COM1 (archaea)
SequenceString: 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

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Macromolecule #4: Ferredoxin-like protein

MacromoleculeName: Ferredoxin-like protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 10.73022 KDa
Recombinant expressionOrganism: Pyrococcus furiosus COM1 (archaea)
SequenceString:
MRIEDKLYLN RYRTDEENPH LKIKDESICA EKCSDRPCVS CCPADVYEWT ESGMEVKFEG CLECGTCRIV CPFGNIEWNY PRGNYGVLY KFG

UniProtKB: Ferredoxin-like protein

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 6 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #6: MENAQUINONE-7

MacromoleculeName: MENAQUINONE-7 / type: ligand / ID: 6 / Number of copies: 2 / Formula: MQ7
Molecular weightTheoretical: 648.999 Da
Chemical component information

ChemComp-MQ7:
MENAQUINONE-7

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris
200.0 mMNaClSodium Chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R2/1 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2471763
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 285377
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7koe:
Electron bifurcating flavoprotein Fix/EtfABCX

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