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Open data
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Basic information
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Title | Cryo-EM map of the Thermococcus sibiricus NfnABC complex | |||||||||
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![]() | Flavin-based electron bifurcation / Bfu family / Nfn-ABC / cryo-EM structures / flavo-FeS cluster / ELECTRON TRANSPORT | |||||||||
Function / homology | ![]() iron-sulfur cluster binding / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
![]() | Xiao X / Li H | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 102.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.4 KB 24.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 109.9 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() | 118 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 769.9 KB | Display | ![]() |
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Full document | ![]() | 769.4 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9n5uMC ![]() 9n5vC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_49039_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_49039_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_49039_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Ternary complex of the Tsi NfnABC complex
Entire | Name: Ternary complex of the Tsi NfnABC complex |
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Components |
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-Supramolecule #1: Ternary complex of the Tsi NfnABC complex
Supramolecule | Name: Ternary complex of the Tsi NfnABC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: NfnA
Macromolecule | Name: NfnA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 107.91282 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: NfnB
Macromolecule | Name: NfnB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 66.237703 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: NfnC
Macromolecule | Name: NfnC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.382266 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNIQLEYIYH YEPNPSSLIP LLQKTQETFG YLPKEALEEI SRYLKVPLSR VYGVATFYAQ FRFEPLGKYV IKICHGTACH VNGAVNISQ AIREEVGIEE GQTTVDGLIT LERVACLGCC SLAPVIMINE KVYGKLTPDK VRKIIRNLKE GKLNV UniProtKB: NADH:ubiquinone oxidoreductase, subunit E |
-Macromolecule #4: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 8 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 1 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ![]() ChemComp-FAD: |
-Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ![]() ChemComp-FES: |
-Macromolecule #7: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: FMN |
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Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ![]() ChemComp-FMN: |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-9n5u: |