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- EMDB-55279: HdrBC-focused map of the mobile arm under state 1 substate a of M... -

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Basic information

Entry
Database: EMDB / ID: EMD-55279
TitleHdrBC-focused map of the mobile arm under state 1 substate a of M. marburgensis
Map dataSharpened map obtained after HdrBC-focused refinement, under state 1 substate a
Sample
  • Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / 4 iron, 4 sulfur cluster binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. ...CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / 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
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 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_55279.png

Downloads & links

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Map

FileDownload / File: emd_55279.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map obtained after HdrBC-focused refinement, under state 1 substate a
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: 0.15
Minimum - Maximum-0.5825069 - 1.7163144
Average (Standard dev.)0.00009695301 (±0.024506494)
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_55279_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 HdrBC-focused refinement, under state...

Fileemd_55279_additional_1.map
AnnotationUnsharpened map obtained after HdrBC-focused refinement, under state 1 substate a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the HdrBC-focused map, state 1 substate a

Fileemd_55279_half_map_1.map
AnnotationHalf map B of the HdrBC-focused map, state 1 substate a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the HdrBC-focused map, state 1 substate a

Fileemd_55279_half_map_2.map
AnnotationHalf map A of the HdrBC-focused map, state 1 substate 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 : (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: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

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

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 1 / 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 #2: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 2 / 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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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: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12602
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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