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- EMDB-55282: MvhAGD-focused map of the mobile arm under state 1 substate b of ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55282
TitleMvhAGD-focused map of the mobile arm under state 1 substate b of M. marburgensis
Map dataSharpened MvhAGD-focused map, state 1 substate 2
Sample
  • Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: F420-non-reducing hydrogenase iron-sulfur subunit D
    • Protein or peptide: F420-non-reducing hydrogenase subunit A
    • Protein or peptide: F420-non-reducing hydrogenase subunit G
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / ferredoxin hydrogenase activity / nickel cation binding / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
: / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit ...: / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit
Similarity search - Domain/homology
F420-non-reducing hydrogenase subunit A / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsSan Segundo-Acosta P / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science Advances / Year: 2026
Title: Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens
Authors: San Segundo-Acosta P / Nomura S / Fernandes-Queiroz JP / Protasov E / Kahnt J / Kaneko M / Hochberg G / Shima S / Murphy BJ
History
DepositionOct 3, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55282.png

Downloads & links

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Map

FileDownload / File: emd_55282.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened MvhAGD-focused map, state 1 substate 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 401.1 Å		0.84 Å/pix.
x 480 pix.
= 401.1 Å		0.84 Å/pix.
x 480 pix.
= 401.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.7828078 - 1.8539695
Average (Standard dev.)0.00034732497 (±0.04110071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 401.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55282_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened MvhAGD-focused map, state 1 substate 2

Fileemd_55282_additional_1.map
AnnotationUnsharpened MvhAGD-focused map, state 1 substate 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the MvhAGD-focused map, state 1 substate 2

Fileemd_55282_half_map_1.map
AnnotationHalf map A of the MvhAGD-focused map, state 1 substate 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the MvhAGD-focused map, state 1 substate 2

Fileemd_55282_half_map_2.map
AnnotationHalf map B of the MvhAGD-focused map, state 1 substate 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

EntireName: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
Components
  • Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: F420-non-reducing hydrogenase iron-sulfur subunit D
    • Protein or peptide: F420-non-reducing hydrogenase subunit A
    • Protein or peptide: F420-non-reducing hydrogenase subunit G

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Supramolecule #1: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

SupramoleculeName: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: F420-non-reducing hydrogenase iron-sulfur subunit D

MacromoleculeName: F420-non-reducing hydrogenase iron-sulfur subunit D / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString:
MAEDDIKIVM FCCNWCSYGG ADTAGTARMQ YPTNIRVIRV MCSGRIEPQF VFKAFREGAD GVLVTGCHH GDCHYDAGNY KLDRRMRLIY KLADELGIGR ERIHHDWISA SEGEKFAETV K MMVDRIRA LGPSPIKKQL AEA

UniProtKB: F420-non-reducing hydrogenase iron-sulfur subunit D

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Macromolecule #2: F420-non-reducing hydrogenase subunit A

MacromoleculeName: F420-non-reducing hydrogenase subunit A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHH LAAAKAVDAC FGFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF I AGKDRKTR NVFQIIKDAP DVALQAIELR KNALEIVRAT GGRPIHPTSS ...String:
MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHH LAAAKAVDAC FGFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF I AGKDRKTR NVFQIIKDAP DVALQAIELR KNALEIVRAT GGRPIHPTSS TPGGISTELD DE TQKDLLQ KAQRNVELAE ATLELAVPIF EENIDLVNSL GNIETYHTGL VKNGVWDVYD GIV RIKDKE GNLFREFKPA DYADTIAEHV KPYSWLKFPY IKDLGYPDGV YRVSPLSRLN VADK MPDAA PKAQDYFKEF QDKFGYAQQT LLYHWARLIE VLACAECAAD ALEGDLSGEK FPDSL ERQA GDGVGIVEAP RGTLTHHYTC DENGLITKAN IVVATIQNNP AMEMGIQKVA QDYIKP GVE VDDKIFNLME MVIRAYDPCL SCATHTIDSQ MRLATLEVYD SEGDLVKRI

UniProtKB: F420-non-reducing hydrogenase subunit A

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Macromolecule #3: F420-non-reducing hydrogenase subunit G

MacromoleculeName: F420-non-reducing hydrogenase subunit G / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDEN REFAEELREK AKFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP N EEGVIPSE DVPHLEGRVK PLGEVIDVDF EVPGCPPRSD VAAEVVMALL ...String:
MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDEN REFAEELREK AKFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP N EEGVIPSE DVPHLEGRVK PLGEVIDVDF EVPGCPPRSD VAAEVVMALL KGEEIELPST NL CEVCPRE KPPEGLAMDF IKRQFEVGKP EDDLCLIPQG LICMGPATVS ICGAECPSIA IPC RGCYGP TARVEDQGAK MISAIASDYK VEEDKTVDPE EVAEQLDDIV GTFYTFTLPA ALIP MKIKK EGK

UniProtKB: F420-non-reducing hydrogenase subunit G

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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

Concentration1.2 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 18777 / Average exposure time: 3.55 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 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: 917008
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17398
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2
Details: 3D-classification without alignment with RELION used before final local refinements and CTF correction
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Generated using ModelAngelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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