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- EMDB-55271: Focused map of the FmdABCFG(2) unit of the Mvh-Hdr-Fmd complex of... -

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Basic information

Entry
Database: EMDB / ID: EMD-55271
TitleFocused map of the FmdABCFG(2) unit of the Mvh-Hdr-Fmd complex of M. marburgensis
Map dataSharpened map obtained from the focused 3d-refinement of the FmdABCFG complex
Sample
  • Complex: FmdABCGF(2) region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit A
    • Protein or peptide: molybdenum containing formylmethanofuran dehydrogenase, subunit B
    • Protein or peptide: molybdenum containing formylmethanofuran dehydrogenase, subunit C
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit F
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit G
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / methanogenesis, from carbon dioxide / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding / molybdopterin cofactor binding / NADH dehydrogenase activity / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / methanogenesis, from carbon dioxide / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding / molybdopterin cofactor binding / NADH dehydrogenase activity / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
Formylmethanofuran dehydrogenase, fused subunit C/D / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily ...Formylmethanofuran dehydrogenase, fused subunit C/D / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Metal-dependent hydrolase, composite domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Metal-dependent hydrolase / 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
Tungsten formylmethanofuran dehydrogenase, subunit F / Tungsten formylmethanofuran dehydrogenase, subunit G / Tungsten formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B / Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 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_55271.png

Downloads & links

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Map

FileDownload / File: emd_55271.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map obtained from the focused 3d-refinement of the FmdABCFG complex
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: 0.389
Minimum - Maximum-1.1697636 - 3.1042402
Average (Standard dev.)0.0012952123 (±0.049724225)
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_55271_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 from the focused 3D-refinement of...

Fileemd_55271_additional_1.map
AnnotationUnsharpened map obtained from the focused 3D-refinement of the FmdABCFG complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55271_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_55271_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 : FmdABCGF(2) region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bi...

EntireName: FmdABCGF(2) region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
Components
  • Complex: FmdABCGF(2) region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit A
    • Protein or peptide: molybdenum containing formylmethanofuran dehydrogenase, subunit B
    • Protein or peptide: molybdenum containing formylmethanofuran dehydrogenase, subunit C
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit F
    • Protein or peptide: tungsten formylmethanofuran dehydrogenase, subunit G

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

SupramoleculeName: FmdABCGF(2) 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: tungsten formylmethanofuran dehydrogenase, subunit A

MacromoleculeName: tungsten formylmethanofuran dehydrogenase, subunit A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MEYIIKNGFV YCPLNNVDGE KMDICVRDGK IVESVSDSAK VIDASGKIVM PGGVDPHSHI AGAKVNVGRM YRPEDSRRD AEKFKAGRAG SGFSVPSTFM TGYRYAQMGY TTAMEAAMPP LLARHTHEEF HDTPIIDHAA Y PLFGNNWF VMEYLKEGDV DACAAYASWL ...String:
MEYIIKNGFV YCPLNNVDGE KMDICVRDGK IVESVSDSAK VIDASGKIVM PGGVDPHSHI AGAKVNVGRM YRPEDSRRD AEKFKAGRAG SGFSVPSTFM TGYRYAQMGY TTAMEAAMPP LLARHTHEEF HDTPIIDHAA Y PLFGNNWF VMEYLKEGDV DACAAYASWL LKATKGYTIK IVNPAGTEAW GWGGNVHGIH DPAPYFDITP AE IIKGLAE VNEKLQLPHS IHLHCNDLGH PGNYETTLAS FDVPKNIKAN PATGERDTVL YATHVQFHSY GGT TWRDFV SEAPKIADYV NKNDHIVIDV GQITLDETTT MTADGPMEYD LHSLNGLKWA NCDVELETGS GVVP FIYSA RAPVPAVQWA IGMELFLLID DPAKVCLTTD SPNAGPFTRY PRVIAWLMSN KYRMNLIEGE LHKWA QRKS TIATVDREYT FSEIAQITRS TSAKVLGLSE TKGHLGVGAD ADIAVYNINP ETVDPSVDYM AIEEGF SRA AYVLKDGEIV VKDGEVVASP HGRTYWVDTR VDESTYNEVL AKVESKFKQY YSVNFANYPV QDEYLPK SA PVKGVML

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit A

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Macromolecule #2: molybdenum containing formylmethanofuran dehydrogenase, subunit B

MacromoleculeName: molybdenum containing formylmethanofuran dehydrogenase, subunit B
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MSVYKNVTCP VCGGSCDDIE VLYDGKTIKT RNACRMGNAK FQEMVSSHRI LRPQIKTESG FRSAEWDEAL DAAAEILTE SKRPTLFMGS EMSTEAMAAG LELGEYLNAM VDSNATICHG PTLMGIQEAG QSAATAGEIK N RADVIIYW GTNVMDSMPR HMSRYSIFMR ...String:
MSVYKNVTCP VCGGSCDDIE VLYDGKTIKT RNACRMGNAK FQEMVSSHRI LRPQIKTESG FRSAEWDEAL DAAAEILTE SKRPTLFMGS EMSTEAMAAG LELGEYLNAM VDSNATICHG PTLMGIQEAG QSAATAGEIK N RADVIIYW GTNVMDSMPR HMSRYSIFMR GFFRERGKKD RTVISVDPRE TATTKASDIH LQLKPNSDYE LF SALLTVI RGNEPHRSIE SITGISVETI KEVADIMLNA QFGAIYGGLG LASSEGKHRN VEMVLKLVAA LNE HTKFTI GAIRGHCNVA GFNQVASWEY GFPFGVDFTR GYPRYNPGET TIVDLLQRKE SDAVLVICSD LGAH LPKEC VEYMKEIPVI CIDIAPCPTT LVSDVVIPGV IDAMESSGTF YRFDNVPIHH KAFTTSPFPE TESNE HTLR QILERVKSIK GE

UniProtKB: formylmethanofuran dehydrogenase subunit B

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Macromolecule #3: molybdenum containing formylmethanofuran dehydrogenase, subunit C

MacromoleculeName: molybdenum containing formylmethanofuran dehydrogenase, subunit C
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: MGFVLVPKSD FQIPLEADTI RPDLFEGLDL DEIRSLQVYE GNIKRPLGEF FEIAETSHED QLIRIDGDVS RVKYIGSGM KSGKIIINGD VGLQLGCEMK GGEIEVNGNV SSWIGMEMHG GTIKINGNAG DYVGCAYRGE W RGMKGGKI IIQGNAGNNI GGGMMAGEIY ...String:
MGFVLVPKSD FQIPLEADTI RPDLFEGLDL DEIRSLQVYE GNIKRPLGEF FEIAETSHED QLIRIDGDVS RVKYIGSGM KSGKIIINGD VGLQLGCEMK GGEIEVNGNV SSWIGMEMHG GTIKINGNAG DYVGCAYRGE W RGMKGGKI IIQGNAGNNI GGGMMAGEIY IGGDAGNFCG IRMNGGEITV RGDAGRAPGA EMVSGIIKIH GR ISSLLPG FKEISTFKED GSLMILFKGD LSEKNPEGNL YINYNKNLHI LENETDEGRV ITKKGIKVIY NSG STIREG QIIKGGNKLT DDYIDECARC CISPEDYKLL GEPENVVVSS HGNEVVLRAV EDPGIQMGTI FIPR GIWAN VLTPPYTEST GSPMYKGVPV YLRKASQGER ILSAEELVEE YGVGK

UniProtKB: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C

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Macromolecule #4: tungsten formylmethanofuran dehydrogenase, subunit F

MacromoleculeName: tungsten formylmethanofuran dehydrogenase, subunit F / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString: METTEVIEGK NITVERTGEE NRKLIFQDCL CAVCGLCGEI CPVSAIEVNP TGAMVRTEQD ESKILIDENK CVLCGMCSS ICPFQALDLQ IDGTSIKELA EYPKILKSAE IDDETCIQCK ACETACPQDA ITITRELPER K DLITGEIE IDKDTCIYCG MCEEMCPVDA ...String:
METTEVIEGK NITVERTGEE NRKLIFQDCL CAVCGLCGEI CPVSAIEVNP TGAMVRTEQD ESKILIDENK CVLCGMCSS ICPFQALDLQ IDGTSIKELA EYPKILKSAE IDDETCIQCK ACETACPQDA ITITRELPER K DLITGEIE IDKDTCIYCG MCEEMCPVDA IEIEHQIPSS SSPTVATDIN VDEDKCVHCG ICKRICPVDA IM QVCRICP YGEYEIKVPE VTGTSYIDPE LCVNCGWCQE ICPVDAATVT KPFEGELIID QDTCQACETC VMA CPCNVL SFPKPEKSGE KPTKLYKDER FCIYCGACER SCPVNAIEVK RSRINTTPIK SKAWKNAFES LLK

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit F

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Macromolecule #5: tungsten formylmethanofuran dehydrogenase, subunit G

MacromoleculeName: tungsten formylmethanofuran dehydrogenase, subunit G / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
SequenceString:
MAIGLKAYPE LCHGCGNCVI ACPVNALRSP EVAGGKGPTD DVEIIMIVED GVVNIKNPDL CGKCGTCVES CPVDAIRLE ELE

UniProtKB: Tungsten formylmethanofuran dehydrogenase, 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: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105282
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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