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- EMDB-19535: State 1 Hdr-focused map Elp-Hdr -

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Basic information

Entry
Database: EMDB / ID: EMD-19535
TitleState 1 Hdr-focused map Elp-Hdr
Map dataHdr focused map of the conformational state 1 of the Elp-Hdr complex
Sample
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit C
KeywordsRedox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase / Oxidoreductase
Function / homology
Function and homology information


H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / Alanine dehydrogenase/PNT, C-terminal domain / 4Fe-4S dicluster domain ...CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / Alanine dehydrogenase/PNT, C-terminal domain / 4Fe-4S dicluster domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / Alpha-helical ferredoxin / 4Fe-4S binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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
Similarity search - Domain/homology
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSan Segundo-Acosta P / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2025
Title: Electron flow in hydrogenotrophic methanogens under nickel limitation.
Authors: Shunsuke Nomura / Pablo San Segundo-Acosta / Evgenii Protasov / Masanori Kaneko / Jörg Kahnt / Bonnie J Murphy / Seigo Shima /
Abstract: Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO ...Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO reduction are generated by a flavin-based electron-bifurcation reaction catalysed by heterodisulfide reductase (Hdr) complexed with the associated [NiFe]-hydrogenase (Mvh). F-reducing [NiFe]-hydrogenase (Frh) provides electrons to the methanogenic pathway through the electron carrier F (ref. ). Here we report that under strictly nickel-limited conditions, in which the nickel concentration is similar to those often observed in natural habitats, the production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly downregulated. The Frh reaction is substituted by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F-dependent electron-donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions. Biochemical and structural characterization of Elp-Hdr complexes confirms the electronic interaction between Elp and Hdr. The conservation of the genes encoding Elp and Hmd in CO-reducing hydrogenotrophic methanogens suggests that the Hmd system is an alternative pathway for electron flow in CO-reducing hydrogenotrophic methanogens under nickel-limited conditions.
History
DepositionFeb 2, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19535.png

Downloads & links

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Map

FileDownload / File: emd_19535.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHdr focused map of the conformational state 1 of the Elp-Hdr complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.613
Minimum - Maximum-1.6205294 - 3.10128
Average (Standard dev.)0.00035225798 (±0.06989745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 374.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A of the Hdr focused map of...

Fileemd_19535_half_map_1.map
AnnotationHalf A of the Hdr focused map of the conformational state 1 of the Elp-Hdr complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B of the Hdr focused map of...

Fileemd_19535_half_map_2.map
AnnotationHalf B of the Hdr focused map of the conformational state 1 of the Elp-Hdr complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F420-dependent electron-donating proteins- heterodisulfide reduct...

EntireName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
Components
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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Supramolecule #1: F420-dependent electron-donating proteins- heterodisulfide reduct...

SupramoleculeName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: CoB-CoM heterodisulfide,ferredoxin reductase subunit A

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFRR CVEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL ...String:
MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFRR CVEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL ADMGFKTYMV EKRPSISGRM GQLDKTFPTL DCSMCILAPK MVDVGKHDNI ELITYAEVKE VDGYIGNFKV KIEKKPRYID EELCTGCGSC VEVCPIEMPN YFDEGIGMTK AVYIPFPQAV PLCATIDKDY CIECMLCDEV CERGAVKHDQ EPEEIEIEVG TIIVATGYDA YDPTEKLEYG YGRHTNVITG LELERMINAS GPTDGKVLKP SDGEKPKRVA FIHCVGSRDE QIGKPYCSRV CCMYIMKNAQ LIKDKMPDTE VTLYYMDIRA FGKGFEEFYK RSQEKYGIKF IRGRPAEVIE NPDLTLTVRS EDTLLGKVTE YDYDMVVLGV GLVPPEGAET LRQTIGLSKS ADGFLMEAHP KLRPVDTLTD GVYLAGVAQG PKDIPDAVAQ ASGAAARAAI PMVKGEVEIE PIIAVTDSDV CGGCEVCIEL CPFGAISIEE GHANVNVALC KGCGTCVAAC PSGAMDQQHF KTEQIMAQIE AALNEPASK

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

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Macromolecule #2: CoB-CoM heterodisulfide,ferredoxin reductase subunit A

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFRR CVEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL ...String:
MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFRR CVEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL ADMGFKTYMV EKRPSISGRM GQLDKTFPTL DCSMCILAPK MVDVGKHDNI ELITYAEVKE VDGYIGNFKV KIEKKPRYID EELCTGCGSC VEVCPIEMPN YFDEGIGMTK AVYIPFPQAV PLCATIDKDY CIECMLCDEV CERGAVKHDQ EPEEIEIEVG TIIVATGYDA YDPTEKLEYG YGRHTNVITG LELERMINAS GPTDGKVLKP SDGEKPKRVA FIHCVGSRDE QIGKPYCSRV CCMYIMKNAQ LIKDKMPDTE VTLYYMDIRA FGKGFEEFYK RSQEKYGIKF IRGRPAEVIE NPDLTLTVRS EDTLLGKVTE YDYDMVVLGV GLVPPEGAET LRQTIGLSKS ADGFLMEAHP KLRPVDTLTD GVYLAGVAQG PKDIPDAVAQ ASGAAARAAI PMVKGEVEIE PIIAVTDSDV CGGCEVCIEL CPFGAISIEE GHANVNVALC KGCGTCVAAC PSGAMDQQHF KTEQIMAQIE AALNEPASK

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Macromolecule #3: CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCVDEC LEKLEELDRL APGSG

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

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Macromolecule #4: CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCVDEC LEKLEELDRL APGSG

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Macromolecule #5: CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString:
MTLLQREENI IRKGNIDKEF SEKIKAAGGD SLEYCFQCGT CTGSCPSGRR TPYRVRQIIR KANVGLKDEI ISDPTLWMCT TCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV GSFVIKTGHG VPINDATMEL RKAVGLGELP PTTHQFPEAL E EVQKIIKA TGFDQLIGYN WETGELE

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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Macromolecule #6: CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString:
MTLLQREENI IRKGNIDKEF SEKIKAAGGD SLEYCFQCGT CTGSCPSGRR TPYRVRQIIR KANVGLKDEI ISDPTLWMCT TCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV GSFVIKTGHG VPINDATMEL RKAVGLGELP PTTHQFPEAL E EVQKIIKA TGFDQLIGYN WETGELE

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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

Concentration1 mg/mL
BufferpH: 7.6
Details: 50 mM Tris-HCl pH 7.6 containing 400 mM Ammonium sulfate.
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7768 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
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: 1300000
Details: A Topaz-trained model was used for particle picking
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4)
Details: C2_symmetry_expanded particles Final local refinement in Cryosparc after classification
Number images used: 76528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Automated-based model building using Model-Angelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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