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- EMDB-49039: Cryo-EM map of the Thermococcus sibiricus NfnABC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49039
TitleCryo-EM map of the Thermococcus sibiricus NfnABC complex
Map data
Sample
  • Complex: Ternary complex of the Tsi NfnABC complex
    • Protein or peptide: NfnA
    • Protein or peptide: NfnB
    • Protein or peptide: NfnC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION
KeywordsFlavin-based electron bifurcation / Bfu family / Nfn-ABC / cryo-EM structures / flavo-FeS cluster / ELECTRON TRANSPORT
Function / homology
Function and homology information


NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / Alpha-helical ferredoxin / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. ...NADP-reducing hydrogenase subunit HndA / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / Alpha-helical ferredoxin / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / 2Fe-2S iron-sulfur cluster binding domain / NuoE domain / FAD/NAD(P)-binding domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Pyridine nucleotide-disulphide oxidoreductase / 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-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 / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH:ubiquinone oxidoreductase, NADH-binding subunit F / NADH:ubiquinone oxidoreductase, subunit E / Glutamate synthase beta chain-related oxidoreductase, containing 2Fe-2S and 4Fe-4S clusters
Similarity search - Component
Biological speciesThermococcus sibiricus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsXiao X / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: J Biol Chem / Year: 2025
Title: Cryo-EM structures define the electron bifurcating flavobicluster and ferredoxin binding site in an archaeal Nfn-Bfu transhydrogenase.
Authors: Xiansha Xiao / Gerrit J Schut / Xiang Feng / Diep M N Nguyen / Haiyan Huang / Shuning Wang / Huilin Li / Michael W W Adams /
Abstract: Flavin-based electron bifurcation couples exergonic and endergonic redox reactions in one enzyme complex to circumvent thermodynamic barriers and minimize free energy loss. Two unrelated enzymes ...Flavin-based electron bifurcation couples exergonic and endergonic redox reactions in one enzyme complex to circumvent thermodynamic barriers and minimize free energy loss. Two unrelated enzymes designated NfnSL and NfnABC catalyze the NADPH-dependent reduction of ferredoxin and NAD. Bifurcation by NfnSL resides with a single FAD but the bifurcation mechanism of NfnABC, which represents the diverse and ubiquitous Bfu enzyme family, is completely different and largely unknown. Using cryo-EM structures of an archaeal NfnABC, we show that its bifurcation site is a flavobicluster consisting of FMN, one [4Fe-4S] and one [2Fe-2S] cluster where zinc atoms replace two additional clusters previously identified in other Bfu enzymes. NADH binds to the flavobicluster site of NfnABC and induces conformational changes that allow ferredoxin to bind between the C-terminal domains of NfnC and NfnB. Site-directed mutational analyses support the proposed mechanism that is likely conserved in all members of the Bfu enzyme family.
History
DepositionFeb 4, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49039.png

Downloads & links

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Map

FileDownload / File: emd_49039.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 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: 1.0
Minimum - Maximum-0.13476285 - 20.913363
Average (Standard dev.)-0.03344885 (±0.6033912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49039_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49039_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49039_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of the Tsi NfnABC complex

EntireName: Ternary complex of the Tsi NfnABC complex
Components
  • Complex: Ternary complex of the Tsi NfnABC complex
    • Protein or peptide: NfnA
    • Protein or peptide: NfnB
    • Protein or peptide: NfnC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION

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Supramolecule #1: Ternary complex of the Tsi NfnABC complex

SupramoleculeName: Ternary complex of the Tsi NfnABC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermococcus sibiricus (archaea)

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Macromolecule #1: NfnA

MacromoleculeName: NfnA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus sibiricus (archaea)
Molecular weightTheoretical: 107.91282 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString: MPRRRVSEMV KITVNGKEFE APKDKSLIEF LREITHVPGF CYTEAFDPYG SCRLCLVQTP RGITTSCTLK PMEGLSIETL SDEIIEMRK TALELILSDH YGDCIGPCQN GCPAHSDVQG YLALIAMGRY HEAVKLMKEK YILPAVLGRV CPAFCEEECR R NLVEEPLA ...String:
MPRRRVSEMV KITVNGKEFE APKDKSLIEF LREITHVPGF CYTEAFDPYG SCRLCLVQTP RGITTSCTLK PMEGLSIETL SDEIIEMRK TALELILSDH YGDCIGPCQN GCPAHSDVQG YLALIAMGRY HEAVKLMKEK YILPAVLGRV CPAFCEEECR R NLVEEPLA IRQLKRFAAD YDLENGPWMP EIPPSTGKRI AVVGGGPAGL ACAYYLRTMG HDVTIFDAMP HLGGMMRYGI PP YRLPKDV LDKDIATVIN TGIEVKTNTA LGKDIALEEL REQYDAVFLG VGAWKSRKMG IEGEDLDGVI HGTEFLRKVN MGE KVELGK RVIVVGGGNT AMDVARTALR LGADVTVVYR RSKSEMPANS REVEEAEEEG VKFMFLTNPV KIIGKEKVEE VELI KMKLG EPDASGRRRP MPIEGSEFRV KVDNVILAIG QYCDEEFLRT IGIEAKRGRV LVDEVTLQTN KEGVFAGGDL VLGPS TVIE SIATGRRAAI MIDLYLKGKL EKAREVLLDP SKHIEEVIYD EDLYRVLFDL RPYNHWKKVT EKDYEHVERK PRVKVK LLD PEIRKSNFKE VEPTMDEETV LTEAQRCMSC GCMEVFRCKL REYATLYDAK QDAFVGEQNK FEIDETHPNV VLDNNKC VL CGQCVNFTHE IAREGIVDYL FRGFKTYIGP QLGERLEDQK GVFIGELTDI CPVGAITEKL PFVKPGPWKT QPVKTVCN G CSFACEMNIE VYNDILVRAS SRKDSWNGYI CDYCRFERPW AQDIAQPILK GNAVSWEDAE KFLEEKECAL ILTPSLTNE EIMFLKELAE RKGIPIGSTI DGEGSTATLE DIRNAKRVLL KVNIEKYPLL KLLLKGKEIV EEGYEVAIIE GPAEPMDVPT LILHDGVNA TGLIKAGVTG IPEAKAYVVI GNSPAISKLK GEYLILPSGL WAEKEGTVTN AFGMDLKVKK ARKAHYDVKS L FNF

UniProtKB: Glutamate synthase beta chain-related oxidoreductase, containing 2Fe-2S and 4Fe-4S clusters

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Macromolecule #2: NfnB

MacromoleculeName: NfnB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus sibiricus (archaea)
Molecular weightTheoretical: 66.237703 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString: MSEIKAIAVG MNSCGIAAGA RETYEAVKEE LEKRNLDIKL KIVGCVGMCY REPLLDIITD NEIITYGHVT PDRVPRIIEE HVINGKPIE DWVVKKDWWE NGQRKTWDFD GYFVKQKKIV LENSGYIDPE NIEEYIAAGG YEALKKAFKM KPEEIIDFIT K SGLRGRGG ...String:
MSEIKAIAVG MNSCGIAAGA RETYEAVKEE LEKRNLDIKL KIVGCVGMCY REPLLDIITD NEIITYGHVT PDRVPRIIEE HVINGKPIE DWVVKKDWWE NGQRKTWDFD GYFVKQKKIV LENSGYIDPE NIEEYIAAGG YEALKKAFKM KPEEIIDFIT K SGLRGRGG AGFPTGLKWK FTRDAPGDEK YIVCNADEGD PGAFMDRNVL EGDPHRVIEG MIIGAYAIGA TKGFIYVRAE YP LAIKRLR IALKQAREKG FLGENILGSG FSFEIVIKEG AGAFVCGEET ALIASIEGKR GMPRPRPPYP AQKGLWGRPT NIN NVETWA NVPWIIKHGW EAYAALGTEK SKGTKVFALS GKIKHGGNVE VPMGITLREI LYEIGGGTKT GKKIKAVQLG GPSG GCIPD YLFNTPVDYE SVTATGAIMG SGGMVVMDED TCMVDVAKFF LDFTVKESCG KCTFCRLGTK RMWELLDKIT KGEGA LEDI EKLEKLAPLV KTGSLCGLGQ TAPNPVLTTL KYFKDEYLAH IEGRCPAKVC KPLIKYVIIT EKCTGCTACA IMCPVK AIS GERGKPHLIN QEACIKCGTC YEVCRFNAIE ITDAKKEGE

UniProtKB: NADH:ubiquinone oxidoreductase, NADH-binding subunit F

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Macromolecule #3: NfnC

MacromoleculeName: NfnC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus sibiricus (archaea)
Molecular weightTheoretical: 17.382266 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MNIQLEYIYH YEPNPSSLIP LLQKTQETFG YLPKEALEEI SRYLKVPLSR VYGVATFYAQ FRFEPLGKYV IKICHGTACH VNGAVNISQ AIREEVGIEE GQTTVDGLIT LERVACLGCC SLAPVIMINE KVYGKLTPDK VRKIIRNLKE GKLNV

UniProtKB: NADH:ubiquinone oxidoreductase, subunit E

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 8 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / 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 #6: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / 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 #7: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 18072 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
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: 14943071
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 198898
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9n5u:
Structure of the Thermococcus sibiricus NfnABC complex

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