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- EMDB-55270: Focused map of the MvhB subunit of the Mvh-Hdr-Fmd complex of M. ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55270
TitleFocused map of the MvhB subunit of the Mvh-Hdr-Fmd complex of M. marburgensis
Map dataSharpened map obtained after focused 3D-refinement of the MvhB subunit
Sample
  • Complex: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: Polyferredoxin protein MvhB
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding
Similarity search - Function
4Fe-4S binding domain / : / 3Fe-4S ferredoxin / 4Fe-4S dicluster domain / 4Fe-4S binding domain / 4Fe-4S dicluster domain / 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
Polyferredoxin protein MvhB
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 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_55270.png

Downloads & links

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Map

FileDownload / File: emd_55270.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map obtained after focused 3D-refinement of the MvhB subunit
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: 0.551
Minimum - Maximum-2.6329029 - 4.5824366
Average (Standard dev.)0.00019322429 (±0.054983936)
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_55270_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map obtained after focused 3D-refinement of the...

Fileemd_55270_additional_1.map
AnnotationUnsharpened map obtained after focused 3D-refinement of the MvhB subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B MvhB map

Fileemd_55270_half_map_1.map
AnnotationHalf map B MvhB map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A MvhB map

Fileemd_55270_half_map_2.map
AnnotationHalf map A MvhB map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifur...

EntireName: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
Components
  • Complex: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: Polyferredoxin protein MvhB

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Supramolecule #1: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifur...

SupramoleculeName: FmdABCGF region of the (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: Polyferredoxin protein MvhB

MacromoleculeName: Polyferredoxin protein MvhB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MIVVNKEDCI RCGACQGTCP TAAIEVTPED VIYCDICGGE PKCVDACPTG ALKIEDLVVD EAGNTQGRI VFNPDKCNEC GDCVEVCPPQ ILKLDEGKVK KIPLQGFCVM CQKCVDICPV G VIGVEGIK EPAKVELEIE GPIFIADCVG CGMCVPECPV DAITLEKVGG ...String:
MIVVNKEDCI RCGACQGTCP TAAIEVTPED VIYCDICGGE PKCVDACPTG ALKIEDLVVD EAGNTQGRI VFNPDKCNEC GDCVEVCPPQ ILKLDEGKVK KIPLQGFCVM CQKCVDICPV G VIGVEGIK EPAKVELEIE GPIFIADCVG CGMCVPECPV DAITLEKVGG VIEIDEDTCI KC GVCAQTC PWNAVYISGK KPEKRAKEIR KFELDEEACI GCNTCVEACP GDFIVPKSSN LTV ELPAIC TACGLCEQLC PVDAIDLDVE LGPAKPASEE GLVWDEGKCD FIGACANICP NDAI RVVTR EGMKLPDNEK VDEEPSFAMC TRCGACTMAC PKGALSLVDM DKVIDGEVVK RKRVQ YNPA LCDQCGDCIE ACPYDMLKLT DEKVPLKGFC ILCDQCIPAC PKGALSLK

UniProtKB: Polyferredoxin protein MvhB

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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: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 322503
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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