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- EMDB-48543: Electron-bifurcating Tungstopyranopterin-containing aldehyde oxid... -

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Basic information

Entry
Database: EMDB / ID: EMD-48543
TitleElectron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH
Map data
Sample
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: x 5 types
  • Ligand: x 7 types
Keywordselectron bifurcation / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain ...: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / 4Fe-4S binding domain / : / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH:ubiquinone oxidoreductase 24 kD subunit / NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / NADH:ubiquinone oxidoreductase chain G-like protein / Fe-S-cluster-containing hydrogenase subunit / Aldehyde:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFeng X / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136885 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: To Be Published
Title: An electron bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification
Authors: Feng X / Schut GJ / Putumbaka S / Li H / Adams MWW
History
DepositionJan 6, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48543.png

Downloads & links

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Map

FileDownload / File: emd_48543.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.3
Minimum - Maximum-32.907550000000001 - 58.548782000000003
Average (Standard dev.)0.00030079178 (±1.2428831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

EntireName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
Components
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: NADH:ubiquinone oxidoreductase chain G-like protein
    • Protein or peptide: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
    • Protein or peptide: NADH:ubiquinone oxidoreductase 24 kD subunit
    • Protein or peptide: Aldehyde:ferredoxin oxidoreductase
    • Protein or peptide: Fe-S-cluster-containing hydrogenase subunit
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: TUNGSTOPTERIN COFACTOR
  • Ligand: MAGNESIUM ION

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Supramolecule #1: electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

SupramoleculeName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: NADH:ubiquinone oxidoreductase chain G-like protein

MacromoleculeName: NADH:ubiquinone oxidoreductase chain G-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 27.662164 KDa
SequenceString: MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRAR KFVLKLLLNR APKSARLNAL ANEYGVSVES RFSFDPDECV RCDRCVRACE TLGPSAIGPA WRGFNKRIVP P FMEPPRQC ...String:
MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRAR KFVLKLLLNR APKSARLNAL ANEYGVSVES RFSFDPDECV RCDRCVRACE TLGPSAIGPA WRGFNKRIVP P FMEPPRQC IGCGACADVC PTGYIECVDE GDERTIWDRK FTLIRCPICG QTYTTEEALK FTGIEDPDAR LCPTCRKREY AS KFRIFVH

UniProtKB: NADH:ubiquinone oxidoreductase chain G-like protein

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Macromolecule #2: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

MacromoleculeName: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 67.862219 KDa
SequenceString: MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQ NVKTKDVPEI VQKTILDGEV IERLLYRDPV TKKTYRSDHE IPFYANQQRL VLRRSGHIDP TSIEDYIATD G YEALCLAF ...String:
MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQ NVKTKDVPEI VQKTILDGEV IERLLYRDPV TKKTYRSDHE IPFYANQQRL VLRRSGHIDP TSIEDYIATD G YEALCLAF KLGPDEIIKQ ITDSYLRGRG GGGFRTGYKW KSCREVDDFP KYVIANGDEG DPGAFMDRSL MEGDPHSVIE GM IIGAYAI GANEGYIYVR NEYPLAVRRL QIAIERAREY GLLGKNILGS GFDFDIQICK GGGAFVCGES SALMRSIEGY PGV PRVKYI HATEQGLWDK PTVLNNVETW ANVPIILMNG VEWYKSLGTE RNSGTKIFAL VGKVKNTGLV EVPMGVTLRK IIYE IGGGT LKDKAFKAVQ TGGPSGGCIP ASLLDLSVDF DTLVKAGSMM GSGGMIVMDE RSCMVDVAKY FIDFLVEESC GKCTP CREG LKVLQKLLHD LTEGKGSLQD VGLLEDTAHE LGKTALCGLG KTAANPVLST LKYFHEEYEE HVEGYCRAGV CTGLFA AKI DKDSCIGCGQ CARTCPVKAI SGEVRGPHVV DALKCIGCGQ CMDVCPTNSI ASSRRVKNA

UniProtKB: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

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Macromolecule #3: NADH:ubiquinone oxidoreductase 24 kD subunit

MacromoleculeName: NADH:ubiquinone oxidoreductase 24 kD subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 17.547506 KDa
SequenceString:
ATSDVAISDI LCRYEKNPRF LLQVLLDVQE KFRYLPTDAM RSVAEYFEIP ESRVFAVATF YKVLSLVPKG EKTIKVCQGT ACHLRGGSQ ILNAISERLK IRAGETTKDG IFTLETVNCL GCCAMAPVMM VGDKVYGKLS VADVARILEA EKEDAIISKA

UniProtKB: NADH:ubiquinone oxidoreductase 24 kD subunit

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Macromolecule #4: Aldehyde:ferredoxin oxidoreductase

MacromoleculeName: Aldehyde:ferredoxin oxidoreductase / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 65.15857 KDa
SequenceString: MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTI AASNSGGYFG PELKYAGYDM IIFEGKSANP VYLWIYNDHV ELRDASHVWG KDSYETTDAL LSETDPEAKV A CIGPAGER ...String:
MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTI AASNSGGYFG PELKYAGYDM IIFEGKSANP VYLWIYNDHV ELRDASHVWG KDSYETTDAL LSETDPEAKV A CIGPAGER LVLFACVMND KHRAAGRTGV GAVMGSKNLK AVVVRGTGGI KLADKEAFLE ALRKARKKIA EHPVTGGGLP AY GTNVLVN VINAAGALPT RNFKEAWFEG ADKISGETMA ETILLKNKAC ASCASACGRV TKAMGEIGEG PEYEAVWAYG AQC GVDNLE AICKANFICN KLGMDPITMG STIGCAMELA ELGLIDEKKA GVSLHWGNAE AIVKLTEDTG YRRGFGEELA LGSY RLGEK YGHPELSMSA KKQEMPAYDP RALQGMGLEY ATSNRGGCHV RGYLTSPEVL GIPEKLDPTD IASKPQWTKT FQDLT AAVD SLGFCLFLTF ALDAGDLAAQ VAPIIGREVT AEELLLAGER IWNLERLFNL KAGISPKEDT LPPRLLNEPI PAGPSK GRV NKLHEMLPKY YELRGWGKNG IPTKERLESL GLLDIAAKYS L

UniProtKB: Aldehyde:ferredoxin oxidoreductase

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Macromolecule #5: Fe-S-cluster-containing hydrogenase subunit

MacromoleculeName: Fe-S-cluster-containing hydrogenase subunit / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 16.593328 KDa
SequenceString:
MEKVLVISPE KCVGCGSCEL ACSLEKEGEC RPSLARVTVY RFEAGANVPM TCQQCDDAPC ISVCKAGALA RDEKNVVQVD SSKCIGCRM CVMACPFGNM SYHWEQSTAI KCDQCNGSPY CVEFCPTKAL DYVPADAISL QKKKEFSARF AKI

UniProtKB: Fe-S-cluster-containing hydrogenase subunit

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 20 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #10: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 10 / Number of copies: 1 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Macromolecule #11: TUNGSTOPTERIN COFACTOR

MacromoleculeName: TUNGSTOPTERIN COFACTOR / type: ligand / ID: 11 / Number of copies: 3 / Formula: PTE
Molecular weightTheoretical: 1.0248 KDa
Chemical component information

ChemComp-PTE:
TUNGSTOPTERIN COFACTOR

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
300.0 mMSodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1042436
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 737000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1)

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