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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 / : / 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
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: To Be Published
Title: An electron bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification
Authors: Feng, X. / Schut, G.J. / Putumbaka, S. / Li, H. / Adams, M.W.W.
History
DepositionJan 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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