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- EMDB-19530: State 2 Hdr-focused map Elp-Hdr -

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Basic information

Entry
Database: EMDB / ID: EMD-19530
TitleState 2 Hdr-focused map Elp-Hdr
Map dataEM focused map of the Hdr dimer Elp state 2, sharpened
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
KeywordsBifurcation / Redox / Methanogenesis / Dehydrogenase / 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-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19530.png

Downloads & links

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Map

FileDownload / File: emd_19530.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM focused map of the Hdr dimer Elp state 2, sharpened
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: 0.432
Minimum - Maximum-1.5541744 - 3.6695702
Average (Standard dev.)0.00031734974 (±0.062453233)
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 map B

Fileemd_19530_half_map_1.map
AnnotationHalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19530_half_map_2.map
Annotationhalf_map_A
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: MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KVKIEKKPRY IDEELCTGCG SCVEVCPIEM PNYFDEGIGM TKAVYIPFPQ AVPLCATIDK DYCIECMLCD EVCERGAVKH DQEPEEIEIE VGTIIVATGY DAYDPTEKLE ...String:
MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KVKIEKKPRY IDEELCTGCG SCVEVCPIEM PNYFDEGIGM TKAVYIPFPQ AVPLCATIDK DYCIECMLCD EVCERGAVKH DQEPEEIEIE VGTIIVATGY DAYDPTEKLE YGYGRHTNVI TGLELERMIN ASGPTDGKVL KPSDGEKPKR VAFIHCVGSR DEQIGKPYCS RVCCMYIMKN AQLIKDKMPD TEVTLYYMDI RAFGKGFEEF YKRSQEKYGI KFIRGRPAEV IENPDLTLTV RSEDTLLGKV TEYDYDMVVL GVGLVPPEGA ETLRQTIGLS KSADGFLMEA HPKLRPVDTL TDGVYLAGVA QGPKDIPDAV AQASGAAARA AIPMVK GEV EIEPIIAVTD SDVCGGCEVC IELCPFGAIS IEEGHANVNV ALCKGCGTCV AACPSGAMDQ QHFKTEQIMA QIEAALNEPA SK

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: MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KVKIEKKPRY IDEELCTGCG SCVEVCPIEM PNYFDEGIGM TKAVYIPFPQ AVPLCATIDK DYCIECMLCD EVCERGAVKH DQEPEEIEIE VGTIIVATGY DAYDPTEKLE ...String:
MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KVKIEKKPRY IDEELCTGCG SCVEVCPIEM PNYFDEGIGM TKAVYIPFPQ AVPLCATIDK DYCIECMLCD EVCERGAVKH DQEPEEIEIE VGTIIVATGY DAYDPTEKLE YGYGRHTNVI TGLELERMIN ASGPTDGKVL KPSDGEKPKR VAFIHCVGSR DEQIGKPYCS RVCCMYIMKN AQLIKDKMPD TEVTLYYMDI RAFGKGFEEF YKRSQEKYGI KFIRGRPAEV IENPDLTLTV RSEDTLLGKV TEYDYDMVVL GVGLVPPEGA ETLRQTIGLS KSADGFLMEA HPKLRPVDTL TDGVYLAGVA QGPKDIPDAV AQASGAAARA AIPMVK GEV EIEPIIAVTD SDVCGGCEVC IELCPFGAIS IEEGHANVNV ALCKGCGTCV AACPSGAMDQ QHFKTEQIMA QIEAALNEPA SK

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

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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 ARNITIAED MGADIMTECN GCFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV R HFAEVLYN DVGLDKLSEL VEKPLNLNVA VHYGCHFLKP SDEINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAED MGADIMTECN GCFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV R HFAEVLYN DVGLDKLSEL VEKPLNLNVA VHYGCHFLKP SDEINIDNPE RPTILDEIVE VT GAKSVEY KDKMMCCGAG GGVRSRDLDV ALDFTREKLT NMKEAGVDAI VNVCPFCHLQ FDV GQMEIK DKFGEEFDIP VLHLAQLLGL AMGLPKEDLV VDAHQVCVDE CLEKLEELDR LAPG SG

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 ARNITIAED MGADIMTECN GCFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV R HFAEVLYN DVGLDKLSEL VEKPLNLNVA VHYGCHFLKP SDEINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAED MGADIMTECN GCFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV R HFAEVLYN DVGLDKLSEL VEKPLNLNVA VHYGCHFLKP SDEINIDNPE RPTILDEIVE VT GAKSVEY KDKMMCCGAG GGVRSRDLDV ALDFTREKLT NMKEAGVDAI VNVCPFCHLQ FDV GQMEIK DKFGEEFDIP VLHLAQLLGL AMGLPKEDLV VDAHQVCVDE CLEKLEELDR LAPG SG

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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 KANVGLKDE IISDPTLWMC TTCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV G SFVIKTGH GVPINDATME LRKAVGLGEL PPTTHQFPEA LEEVQKIIKA TGFDQLIGYN WE TGELE

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 KANVGLKDE IISDPTLWMC TTCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV G SFVIKTGH GVPINDATME LRKAVGLGEL PPTTHQFPEA LEEVQKIIKA TGFDQLIGYN WE TGELE

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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.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
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: These particles were selected using a Topaz model trained with particles selected previously using the CryoSparc template picker
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4)
Details: Particles had been C2_symmetry_expanded and 3D-classified to finally perform Local refinement in CryoSparc
Number images used: 234858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4)
Details: C2_symmetry_expanded particles were classified using Relion to get the different conformations of the Elp mobile arm
FSC plot (resolution estimation)

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Atomic model buiding 1

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

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