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- EMDB-19531: State 2 mobile-arm-focused map Elp-Hdr -

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Basic information

Entry
Database: EMDB / ID: EMD-19531
TitleState 2 mobile-arm-focused map Elp-Hdr
Map dataCryoEM map of the Elp (FdhA2B-MvhD2) flexible arm, conformational state 2
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: F420-dependent electron-donating protein A
    • Protein or peptide: F420-dependent electron-donating protein B
    • Protein or peptide: F420-dependent electron-donating protein C
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
KeywordsBifurcation / Redox / Methanogenesis / Dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin ...F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin oxidoreductase Fe4S4 domain / : / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / 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
Methyl viologen-reducing hydrogenase, subunit D-related protein / formate dehydrogenase (coenzyme F420) / Formate dehydrogenase, alpha subunit
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_19531.png

Downloads & links

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Map

FileDownload / File: emd_19531.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the Elp (FdhA2B-MvhD2) flexible arm, conformational state 2
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: 0.555
Minimum - Maximum-2.467182 - 3.7849205
Average (Standard dev.)0.00016570638 (±0.074356586)
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 A

Fileemd_19531_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_19531_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 : 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: F420-dependent electron-donating protein A
    • Protein or peptide: F420-dependent electron-donating protein B
    • Protein or peptide: F420-dependent electron-donating protein C
    • Protein or peptide: CoB-CoM heterodisulfide,ferredoxin reductase subunit A

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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: F420-dependent electron-donating protein A

MacromoleculeName: F420-dependent electron-donating protein A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MMVKHTLCPS CSAGCGVNIV EMGGAPVGTY PYRRHPVNEG KTCRAGRDCY EIPLMDRVTS PGVKKSGKL SGVNWDEALD KLTELLSSED ISILTTGTLT NEEALKLREI IENFNVKKSG L ITVFPEFD YPEIDIRNIR DYDNIAVIGD AITCAPLIGR RIFHAMAAGA ...String:
MMVKHTLCPS CSAGCGVNIV EMGGAPVGTY PYRRHPVNEG KTCRAGRDCY EIPLMDRVTS PGVKKSGKL SGVNWDEALD KLTELLSSED ISILTTGTLT NEEALKLREI IENFNVKKSG L ITVFPEFD YPEIDIRNIR DYDNIAVIGD AITCAPLIGR RIFHAMAAGA EVRSYDRRDE TR MAVNSGF HITFSDEREV LNDLQQLPGG SLIIITPEIP EIIGPVLEFS SENEFDVLPI FED FNTRGV MQHLPPVNEG EFDSVWLIDP GAAAEPVDVS GKFVLQSIRT EGLTPDIFLP VAAW CEKSG SYTSTAGYTM KLEPALQAPE GVLSDMEIFE RILRAGD

UniProtKB: Formate dehydrogenase, alpha subunit

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Macromolecule #2: F420-dependent electron-donating protein B

MacromoleculeName: F420-dependent electron-donating protein B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSL HCAPTMFGDL ISRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG L NCGGTLAP VSAREMIETF YEIDPDDVVS EEIDRGKFIV ELRDGSHREI ...String:
MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSL HCAPTMFGDL ISRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG L NCGGTLAP VSAREMIETF YEIDPDDVVS EEIDRGKFIV ELRDGSHREI SIDYLEEEGF GR RENCQRC EIMVPRNADL ACGNWGADDG WTFIEVNTER GQEIIEGARS SGYIEAREPS EKM VKIREK IENAMISMAR KFQDKYLDEE YPSLDEWDEY WKRCINCFAC RDACPVCFCR ECEL EKDYL LESDEKAPDP LTFQGVRLSH MGFSCINCGQ CEDVCPMDIP IARIYHRIQK KYRDR TGFT AGVSQELPPM YSGEKD

UniProtKB: formate dehydrogenase (coenzyme F420)

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Macromolecule #3: F420-dependent electron-donating protein C

MacromoleculeName: F420-dependent electron-donating protein C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString:
MSFEPKIVGF CCNWCSYGGA DTAGTARMQY PPNVRIIRVM CSGRVNASMI LKAFSEGADG VFVGGCHIG DCHYDSGNYK WKRRARFIED ILPEFGIDKE RFRWEWISAS EGEKFQKTMQ E FYETVKYL GPLKRAGK

UniProtKB: Methyl viologen-reducing hydrogenase, subunit D-related protein

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

MacromoleculeName: CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 4
Details: Only the N-terminal region: MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQL EIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPE GATEKAKDLVRMAVAKARLLEPLEASK And the C- ...Details: Only the N-terminal region: MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQL EIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPE GATEKAKDLVRMAVAKARLLEPLEASK And the C-terminal region: GEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHFKTEQIMAQIEAALNEPASK are part of the map
Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKEL GINRVVVAAC SPRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP E GATEKAKD LVRMAVAKAR LLEPLEASK VSVDDKALVI GGGVAGIQAA ...String:
MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKEL GINRVVVAAC SPRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP E GATEKAKD LVRMAVAKAR LLEPLEASK VSVDDKALVI GGGVAGIQAA LDLADMGFKT YMVEKRPSIS GRMGQLDKTF PTLDCSMCIL APKMVDVGKH DNIELITYAE VKEVDGYIGN FKVKIEKKPR YIDEELCTGC GSCVEVCPIE MPNYFDEGIG MTKAVYIPFP QAVPLCATID KDYCIECMLC DEVCERGAVK HDQEPEEIEI EVGTIIVATG YDAYDPTEKL EYGYGRHTNV ITGLELERMI NASGPTDGKV LKPSDGEKPK RVAFIHCVGS RDEQIGKPYC SRVCCMYIMK NAQLIKDKMP DTEVTLYYMD IRAFGKGFEE FYKRSQEKYG IKFIRGRPAE VIENPDLTLT VRSEDTLLGK VTEYDYDMVV LGVGLVPPEG AETLRQTIGL SKSADGFLME AHPKLRPVDT LTDGVYLAGV AQGPKDIPDA VAQASGAAAR AAIPMVK GE VEIEPIIAVT DSDVCGGCEV CIELCPFGAI SIEEGHANVN VALCKGCGTC VAACPSGAMD QQHFKTEQIM AQIEAALNEP ASK

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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: Particles picked using a trained model of Topaz
CTF correctionType: 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: The particles had been C2 symmetry expanded Final refinement using 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
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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