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- PDB-9mqx: Electron-bifurcating Tungstopyranopterin-containing aldehyde oxid... -

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Basic information

Entry
Database: PDB / ID: 9mqx
TitleElectron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH
Components
  • (NADH:ubiquinone oxidoreductase ...) x 2
  • Aldehyde:ferredoxin oxidoreductase
  • Fe-S-cluster-containing hydrogenase subunit
  • NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
KeywordsOXIDOREDUCTASE / electron bifurcation
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 / : / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / 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
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / TUNGSTOPTERIN COFACTOR / IRON/SULFUR CLUSTER / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsFeng, X. / Li, H.
Funding support United States, 3items
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: Proc Natl Acad Sci U S A / Year: 2025
Title: An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification.
Authors: Xiang Feng / Gerrit J Schut / Saisuki Putumbaka / Huilin Li / Michael W W Adams /
Abstract: Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes ...Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacterium The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.
History
DepositionJan 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH:ubiquinone oxidoreductase chain G-like protein
B: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
C: NADH:ubiquinone oxidoreductase 24 kD subunit
D: Aldehyde:ferredoxin oxidoreductase
E: Fe-S-cluster-containing hydrogenase subunit
F: Aldehyde:ferredoxin oxidoreductase
G: Fe-S-cluster-containing hydrogenase subunit
H: Aldehyde:ferredoxin oxidoreductase
I: Fe-S-cluster-containing hydrogenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,36145
Polymers358,3289
Non-polymers12,03336
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH:ubiquinone oxidoreductase ... , 2 types, 2 molecules AC

#1: Protein NADH:ubiquinone oxidoreductase chain G-like protein / Tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A


Mass: 27662.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BTZ0
#3: Protein NADH:ubiquinone oxidoreductase 24 kD subunit / Tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C


Mass: 17547.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BTY8

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Protein , 3 types, 7 molecules BDFHEGI

#2: Protein NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / Tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B


Mass: 67862.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BTY9
#4: Protein Aldehyde:ferredoxin oxidoreductase / Tungstopyranopterin-containing aldehyde oxidoreductase subunit L


Mass: 65158.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BTZ2
#5: Protein Fe-S-cluster-containing hydrogenase subunit / Tungstopyranopterin-containing aldehyde oxidoreductase subunit S


Mass: 16593.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BTZ1

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Non-polymers , 7 types, 36 molecules

#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: Fe4S4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe2S2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PTE / TUNGSTOPTERIN COFACTOR


Mass: 1024.800 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C20H22MgN10O14P2S4W / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2300 mMSodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 59 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
2SerialEM4image acquisition
4cryoSPARC4.1CTF correction
9PHENIX1.21model refinement
10cryoSPARC4.1initial Euler assignment
11cryoSPARC4.1final Euler assignment
12cryoSPARC4.1classification
13cryoSPARC4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1042436
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 737000 / Num. of class averages: 2 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00925831
ELECTRON MICROSCOPYf_angle_d1.76335082
ELECTRON MICROSCOPYf_dihedral_angle_d11.3569529
ELECTRON MICROSCOPYf_chiral_restr0.3473924
ELECTRON MICROSCOPYf_plane_restr0.0044479

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