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- EMDB-64063: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreduc... -

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Basic information

Entry
Database: EMDB / ID: EMD-64063
TitleCryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, upper state
Map data
Sample
  • Complex: Na(+)-translocating NADH-quinone reductase
    • Protein or peptide: x 6 types
  • Ligand: x 7 types
KeywordsNa+-NQR / Na+ pump / oxidoreductase / MEMBRANE PROTEIN
Function / homology
Function and homology information


riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FAD binding / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding ...riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FAD binding / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / : / : / NqrA N-terminal barrel-sandwich hybrid domain / NQRA C-terminal domain / NqrA second alpha/beta domain ...Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / : / : / NqrA N-terminal barrel-sandwich hybrid domain / NQRA C-terminal domain / NqrA second alpha/beta domain / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit F / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / : / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / FMN-binding / FMN-binding domain / FMN_bind / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit C
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsIshikawa-Fukuda M / Kishikawa J / Kato T / Murai M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22KJ1795 Japan
Japan Society for the Promotion of Science (JSPS)22H02273 Japan
Japan Society for the Promotion of Science (JSPS)24K08729 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
CitationJournal: bioRxiv / Year: 2025
Title: The Na -pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from relies on dynamic conformational changes.
Authors: Moe Ishikawa-Fukuda / Takehito Seki / Jun-Ichi Kishikawa / Masuya Takahiro / Kei-Ichi Okazaki / Takayuki Kato / Blanca Barquera / Hideto Miyoshi / Masatoshi Murai
Abstract: The Na -pumping NADH-quinone oxidoreductase (Na -NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na -pumping across the membrane. Earlier ...The Na -pumping NADH-quinone oxidoreductase (Na -NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na -pumping across the membrane. Earlier X-ray and cryo-EM structures of Na -NQR from suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na -NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides the first structural insights into the mechanism of Na translocation coupled to electron transfer in Na⁺-NQR.
History
DepositionApr 6, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64063.png

Downloads & links

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Map

FileDownload / File: emd_64063.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.195
Minimum - Maximum-2.1833317 - 3.1263278
Average (Standard dev.)0.00019570133 (±0.05923743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64063_additional_1.map
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Half map: #1

Fileemd_64063_half_map_1.map
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Half map: #2

Fileemd_64063_half_map_2.map
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Sample components

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Entire : Na(+)-translocating NADH-quinone reductase

EntireName: Na(+)-translocating NADH-quinone reductase
Components
  • Complex: Na(+)-translocating NADH-quinone reductase
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit A
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit B
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit C
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit D
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit E
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit F
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: RIBOFLAVIN
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CALCIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Na(+)-translocating NADH-quinone reductase

SupramoleculeName: Na(+)-translocating NADH-quinone reductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 214 KDa

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Macromolecule #1: Na(+)-translocating NADH-quinone reductase subunit A

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 48.680734 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MITIKKGLDL PIAGTPSQVI SDGKAIKKVA LLGEEYVGMR PTMHVRVGDE VKKAQILFED KKNPGVKFTS PVSGKVVEIN RGAKRVLQS VVIEVAGDDQ VTFDKFEANQ LASLNRDAIK TQLVESGLWT AFRTRPFSKV PAIDSTSEAI FVTAMDTNPL A AEPTVVIN ...String:
MITIKKGLDL PIAGTPSQVI SDGKAIKKVA LLGEEYVGMR PTMHVRVGDE VKKAQILFED KKNPGVKFTS PVSGKVVEIN RGAKRVLQS VVIEVAGDDQ VTFDKFEANQ LASLNRDAIK TQLVESGLWT AFRTRPFSKV PAIDSTSEAI FVTAMDTNPL A AEPTVVIN EQSEAFVAGL DVLSALTTGK VYVCKKGTSL PRSQQPNVEE HVFDGPHPAG LAGTHMHFLY PVSADHVAWS IN YQDVIAV GQLFLTGELY TQRVVSLAGP VVNKPRLVRT VMGASLEQLV DSEIMPGEVR IISGSVLSGT KATGPHAYLG RYH LQVSVL REGRDKELFG WAMPGKNKFS VTRSFLGHLF KGQVYNMTTT TNGSDRSMVP IGNYEKVMPL DMEPTLLLRD LCAG DSDSA VRLGALELDE EDLALCTFVC PGKYEYGQLL RECLDKIEKE G

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit A

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Macromolecule #2: Na(+)-translocating NADH-quinone reductase subunit B

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 45.390883 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL ...String:
MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL IVPPTLPLWQ AALGITFGVV VAKEVFGGTG RNFLNPALAG RAFLFFAYPA QISGDLVWTA ADGYSGATAL SQ WAQGGAG ALINNATGQT ITWMDAFIGN IPGSIGEVST LALMIGAAFI VYMGIASWRI IGGVMIGMIL LSTLFNVIGS DTN AMFNMP WHWHLVLGGF AFGMFFMATD PVSASFTNSG KWAYGILIGV MCVLIRVVNP AYPEGMMLAI LFANLFAPLF DHVV VERNI KRRLARYGKQ

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit B

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Macromolecule #3: Na(+)-translocating NADH-quinone reductase subunit C

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 27.65227 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY ...String:
MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY EQGETPGLGG EVENPAWRAQ WVGKKLFDEN HKPAIKIVKG GAPQGSEHGV DGLSGATLTS NGVQNTFDFW LG DMGFGPF LTKVRDGGLN

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit C

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Macromolecule #4: Na(+)-translocating NADH-quinone reductase subunit D

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 22.853217 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ...String:
MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ISNGGWYQPN GLMLLAPSAF FLIGFMIWAI RTFKPEQVEA KE

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit D

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Macromolecule #5: Na(+)-translocating NADH-quinone reductase subunit E

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 21.481678 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD ...String:
MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD VPPGLRGLGI TFITAGLMAL GFMSFSGVQL

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit E

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Macromolecule #6: Na(+)-translocating NADH-quinone reductase subunit F

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit F / type: protein_or_peptide / ID: 6
Details: C-TERMINAL INCLUDES HIS-TAG SEQUENCE AS A PURIFICATION TAG.
Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 45.942363 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI ...String:
MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI QIEAPAHHVK YADFDVPEKY RGDWDKFNLF RYESKVDEPI IRAYSMANYP EEFGIIMLNV RIATPPPNNP NV PPGQMSS YIWSLKAGDK CTISGPFGEF FAKDTDAEMV FIGGGAGMAP MRSHIFDQLK RLKSKRKMSY WYGARSKREM FYV EDFDGL AAENDNFVWH CALSDPQPED NWTGYTGFIH NVLYENYLKD HEAPEDCEYY MCGPPMMNAA VINMLKNLGV EEEN ILLDD FGGHHHHHH

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit F

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Macromolecule #7: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #8: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 8 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN

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Macromolecule #9: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 9 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #11: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 11 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #12: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 12 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H13Cl2NO3Tris-HCl
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid
0.05 %C24H46O11n-DODECYL-beta-D-MALTOSIDE
5.0 mMC21H27N7O14P2NADH
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Image corrector / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.035 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3653368
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.1) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xk3

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1) / Number images used: 1244065
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. v3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7xk3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ud6:
Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, upper state

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