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Entry
Database: EMDB / ID: EMD-19920
TitleCryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii in apo state
Map dataCryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii in apo state
Sample
  • Complex: rhodobacter nitrogen fixation complex from Acetobacterium woodii
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsBioenergetics / anaerobic cryoEM / membrane protein / electron transport / redox-driven sodium pumping
Function / homology
Function and homology information


ferredoxin-NAD+ oxidoreductase (Na+-transporting) / electron transport chain / transmembrane transport / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Ion-translocating oxidoreductase complex, RnfB/RsxB / Ion-translocating oxidoreductase complex, subunit RnfC/RsxC / Ion-translocating oxidoreductase complex subunit E / Ion-translocating oxidoreductase complex, subunit RnfA/RsxA / Ion-translocating oxidoreductase complex Rnf, subunit D / RnfC Barrel sandwich hybrid domain / : / RnfC Barrel sandwich hybrid domain / Ion-translocating oxidoreductase complex, subunit RnfG/RsxG / 4Fe-4S domain ...Ion-translocating oxidoreductase complex, RnfB/RsxB / Ion-translocating oxidoreductase complex, subunit RnfC/RsxC / Ion-translocating oxidoreductase complex subunit E / Ion-translocating oxidoreductase complex, subunit RnfA/RsxA / Ion-translocating oxidoreductase complex Rnf, subunit D / RnfC Barrel sandwich hybrid domain / : / RnfC Barrel sandwich hybrid domain / Ion-translocating oxidoreductase complex, subunit RnfG/RsxG / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / : / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / 4Fe-4S dicluster domain / FMN-binding / FMN-binding domain / FMN_bind / Soluble ligand binding domain / SLBB domain / 4Fe-4S binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 4Fe-4S dicluster domain / 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
Similarity search - Domain/homology
Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B / Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A / Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E / Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G / Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D / Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C
Similarity search - Component
Biological speciesAcetobacterium woodii DSM 1030 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKumar A / Schuller JM
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
European Research Council (ERC)101075992European Union
CitationJournal: Nat Commun / Year: 2025
Title: Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery.
Authors: Anuj Kumar / Jennifer Roth / Hyunho Kim / Patricia Saura / Stefan Bohn / Tristan Reif-Trauttmansdorff / Anja Schubert / Ville R I Kaila / Jan M Schuller / Volker Müller /
Abstract: The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD and pumps ions (Na or H) across a membrane, powering ATP synthesis. ...The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD and pumps ions (Na or H) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na-pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO reductases. Yet, the molecular principles that couple the long-range electron transfer to Na translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na-pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na pump and the reduction of NAD. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.
History
DepositionMar 23, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19920.png

Downloads & links

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Map

FileDownload / File: emd_19920.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii in apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 384 pix.
= 291.84 Å		0.76 Å/pix.
x 384 pix.
= 291.84 Å		0.76 Å/pix.
x 384 pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.13857643 - 0.517592
Average (Standard dev.)-0.00021849733 (±0.007046181)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of sodium pumping Rnf complex from...

Fileemd_19920_additional_1.map
AnnotationCryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii in apo state (sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_19920_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_19920_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rhodobacter nitrogen fixation complex from Acetobacterium woodii

EntireName: rhodobacter nitrogen fixation complex from Acetobacterium woodii
Components
  • Complex: rhodobacter nitrogen fixation complex from Acetobacterium woodii
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E
    • Protein or peptide: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G
  • Ligand: SODIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: RIBOFLAVIN

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Supramolecule #1: rhodobacter nitrogen fixation complex from Acetobacterium woodii

SupramoleculeName: rhodobacter nitrogen fixation complex from Acetobacterium woodii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 20.384445 KDa
SequenceString:
MTLIFIMISA IFVNNFVLSR FLGICPFLGV SKQVETAVGM GVAVTFVMAL ASAITYVVQY AILDPLSLGY LQTIAFILII AALVQLVEM IIKKSSPSLY QALGVYLPLI TTNCAVLGVA LINIQNEYNF IETIFNGVGA ALGFTLAIVL FAGIRERLET S AVPKALEG FPIALLTAGL MAIAFLGFSG MKL

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A

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Macromolecule #2: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 34.762801 KDa
SequenceString: MLNAILVPVG ILGVFGLIFG IGLAIAAKVF EVYEDPRVPL VRAALPGANC GGCGLPGCDA LAANIVGGSA AIDACPVGGA SCAAAVAEI MGMEAGSAVK KVATVICQGT CETAPNRAEY YGEMDCREAM IASGGSKGCR YGCLGYGTCK AVCPFDAIVI G EDGLPKVD ...String:
MLNAILVPVG ILGVFGLIFG IGLAIAAKVF EVYEDPRVPL VRAALPGANC GGCGLPGCDA LAANIVGGSA AIDACPVGGA SCAAAVAEI MGMEAGSAVK KVATVICQGT CETAPNRAEY YGEMDCREAM IASGGSKGCR YGCLGYGTCK AVCPFDAIVI G EDGLPKVD PEKCTSCGKC VEACPKSIMT LVPEAQEVIV KCHNFDKGKI ARLSCTTACI ACGACVKACR FDAITVENNC AK IDYDKCR QCYECVDKCP MNCISGDVEY GKSTAYIIEE NCIACGLCAK NCPVNAITGE IKKPPYVIDH DMCIGCGICF DKC RKSAIE MRPNKTK

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B

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Macromolecule #3: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 47.177758 KDa
SequenceString: MNVKHGTFKG GIHPPYRKES TAEVPLGFGK KPEMVIIPMS LHIGAPCTPI VKKGDTVFLG QRVGEPNGFV SVPVHASVSG KVIAVEERP HASGDRVMSV VIESDGLDTI DPSIKPYGTL EDMDADAIKK MVLNAGIVGL GGATFPTHVK LAIPPDKKVD C VVLNGAEC ...String:
MNVKHGTFKG GIHPPYRKES TAEVPLGFGK KPEMVIIPMS LHIGAPCTPI VKKGDTVFLG QRVGEPNGFV SVPVHASVSG KVIAVEERP HASGDRVMSV VIESDGLDTI DPSIKPYGTL EDMDADAIKK MVLNAGIVGL GGATFPTHVK LAIPPDKKVD C VVLNGAEC EPYLTADHHL MTSQAEKVVM GLKLAMKSVG VEKGFIGVED NKTDAIEALV KAIGNDSRLE VYSLHTKYPQ GA EKQLIAA ITGREVPSGA LPADAGVVVM NVGTAAQIAE SMITGLPLYK RYLTCTGDAI KNPQTIEIRI GVPFQSVIDQ CGG FSSEPG KVISGGPMMG VTQFVTDIPV MKGTSGILCL TKESAKIATP SNCIHCGKCV GVCPIHLQPL NIAEYSQRNM WDKC ESNNA MDCIECGSCS YICPAKRTLV SSIRVAKREI IAQRRKGN

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C

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Macromolecule #4: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 33.762004 KDa
SequenceString: MNELNLTVSS SPHIRAKHST ASIMQNVIIA LLPALAVAGY VFGLWALALV AICVISSVAT EAVIQKLLKK PITVNDWSAV VTGVLLAFN LPINAPWWIG VVGSVFAIAI VKQCFGGLGQ NFINPALAAR AFLLASWPGH MTSTAYIPLT DTVTTATPLA L LKAGETGS ...String:
MNELNLTVSS SPHIRAKHST ASIMQNVIIA LLPALAVAGY VFGLWALALV AICVISSVAT EAVIQKLLKK PITVNDWSAV VTGVLLAFN LPINAPWWIG VVGSVFAIAI VKQCFGGLGQ NFINPALAAR AFLLASWPGH MTSTAYIPLT DTVTTATPLA L LKAGETGS MPSTLDLFTG LNGVYGCIGE ISALALLIGG LYLIYKGIIS WRIPTIYLLT IAIFALLVGQ DPIVHMVSGG VM LGAFFMA TDYASSPVTA KGQIIYAIGC GLITMIIRLY GGYPEGCSYS ILLMNVATPL IERFTKERIY GVTKIKKEAK A

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D

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Macromolecule #5: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 20.544832 KDa
SequenceString: MNFMKNLTRG IIRENPTFVL VLGMCPTLAV TTSAINGMGM GLATMLVLIG SNVAISALRK VIPDNIRIPA FVVVIASFVT IVGMLMKAY VPALDAALGI FIPLIVVNCI ILARAEAFAF SNGIADSFAD AVGMGLGFTL ALTILGSIRE ILGAGSIFGF S LFGAAYEP ...String:
MNFMKNLTRG IIRENPTFVL VLGMCPTLAV TTSAINGMGM GLATMLVLIG SNVAISALRK VIPDNIRIPA FVVVIASFVT IVGMLMKAY VPALDAALGI FIPLIVVNCI ILARAEAFAF SNGIADSFAD AVGMGLGFTL ALTILGSIRE ILGAGSIFGF S LFGAAYEP VLLMILPPGA FLTLGLLIGL INWKTKKA

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E

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Macromolecule #6: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G

MacromoleculeName: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: ferredoxin-NAD+ oxidoreductase (Na+-transporting)
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 21.850881 KDa
SequenceString: METKEKVQID WKVVFKLGLI LFVISAVAAC ALALTNYVTA GTIEEMNVQT NTVARQEVLP KAADFEAVPA KDVEKIASEI GMEKPEELL EVYIGKSNGE VVGYTVKTGP TSGYAGEVQV LTGISADGVI TGITIIKSNE TPGLGAKASG VWNDQFTGKS A KEELVVVK ...String:
METKEKVQID WKVVFKLGLI LFVISAVAAC ALALTNYVTA GTIEEMNVQT NTVARQEVLP KAADFEAVPA KDVEKIASEI GMEKPEELL EVYIGKSNGE VVGYTVKTGP TSGYAGEVQV LTGISADGVI TGITIIKSNE TPGLGAKASG VWNDQFTGKS A KEELVVVK GTTKEGSNEI QAITGSTITS KAVTSGVNMS IQVYQNLSK

UniProtKB: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G

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Macromolecule #7: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 7 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #8: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 10 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #10: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 10 / Number of copies: 3 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #11: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 11 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN

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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: 8
VitrificationCryogen name: ETHANE-PROPANE
DetailsThe Rnf complex was reduced with low potential ferredoxin.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251476
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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