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- EMDB-55296: Structure of the MvhAGD-HdrABC dimer of M. marburgensis under sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-55296
TitleStructure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)
Map dataComposite map of the dimeric structure of MvhAGD-HdrABC in M. marburgensis, under state 2 substate b
Sample
  • Complex: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsOxidoreductase / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / F420-non-reducing hydrogenase iron-sulfur subunit D / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain ...: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / F420-non-reducing hydrogenase iron-sulfur subunit D / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / Cysteine-rich domain / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / 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 / Alpha-helical ferredoxin / 4Fe-4S binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
F420-non-reducing hydrogenase subunit A / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 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 4, 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_55296.png

Downloads & links

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Map

FileDownload / File: emd_55296.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the dimeric structure of MvhAGD-HdrABC in M. marburgensis, under state 2 substate b
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: 5.8
Minimum - Maximum-13.535747000000001 - 54.684780000000003
Average (Standard dev.)0.003643595 (±0.9272607)
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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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: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: F420-non-reducing hydrogenase iron-sulfur subunit D
    • Protein or peptide: F420-non-reducing hydrogenase subunit G
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: F420-non-reducing hydrogenase subunit A
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

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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: #1, #4-#5, #2-#3, #6
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 A

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 72.264961 KDa
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL ...String:
MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL DLADMGFKTY MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KV KIEKKPR YIDEELCTGC GSCVEVCPIE MPNYFDEGIG MTKAVYIPFP QAVPLCATID KDYCIECMLC DEVCERGAVK HDQ EPEEIE IEVGTIIVAT GYDAYDPTEK LEYGYGRHTN VITGLELERM INASGPTDGK VLKPSDGEKP KRVAFIHCVG SRDE QIGKP YCSRVCCMYI MKNAQLIKDK MPDTEVTLYY MDIRAFGKGF EEFYKRSQEK YGIKFIRGRP AEVIENPDLT LTVRS EDTL LGKVTEYDYD MVVLGVGLVP PEGAETLRQT IGLSKSADGF LMEAHPKLRP VDTLTDGVYL AGVAQGPKDI PDAVAQ ASG AAARAAIPMV KGEVEIEPII AVTDSDVCGG CEVCIELCPF GAISIEEGHA NVNVALCKGC GTCVAACPSG AMDQQHF KT EQIMAQIEAA LNEPASK

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

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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 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 33.496371 KDa
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCVDEC LEKLEELDRL APGSG

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

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Macromolecule #3: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 20.548727 KDa
SequenceString:
MTLLQREENI IRKGNIDKEF SEKIKAAGGD SLEYCFQCGT CTGSCPSGRR TPYRVRQIIR KANVGLKDEI ISDPTLWMCT TCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV GSFVIKTGHG VPINDATMEL RKAVGLGELP PTTHQFPEAL E EVQKIIKA TGFDQLIGYN WETGELE

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

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Macromolecule #4: F420-non-reducing hydrogenase iron-sulfur subunit D

MacromoleculeName: F420-non-reducing hydrogenase iron-sulfur subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 15.954442 KDa
SequenceString:
MAEDDIKIVM FCCNWCSYGG ADTAGTARMQ YPTNIRVIRV MCSGRIEPQF VFKAFREGAD GVLVTGCHHG DCHYDAGNYK LDRRMRLIY KLADELGIGR ERIHHDWISA SEGEKFAETV KMMVDRIRAL GPSPIKKQLA EA

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

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Macromolecule #5: F420-non-reducing hydrogenase subunit G

MacromoleculeName: F420-non-reducing hydrogenase subunit G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 33.786582 KDa
SequenceString: MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDENR EFAEELREKA KFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP NEEGVIPSED VPHLEGRVKP LGEVIDVDFE VPGCPPRSDV A AEVVMALL ...String:
MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDENR EFAEELREKA KFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP NEEGVIPSED VPHLEGRVKP LGEVIDVDFE VPGCPPRSDV A AEVVMALL KGEEIELPST NLCEVCPREK PPEGLAMDFI KRQFEVGKPE DDLCLIPQGL ICMGPATVSI CGAECPSIAI PC RGCYGPT ARVEDQGAKM ISAIASDYKV EEDKTVDPEE VAEQLDDIVG TFYTFTLPAA LIPMKIKKEG K

UniProtKB: F420-non-reducing hydrogenase subunit G

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Macromolecule #6: F420-non-reducing hydrogenase subunit A

MacromoleculeName: F420-non-reducing hydrogenase subunit A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 52.905051 KDa
SequenceString: MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHHL AAAKAVDACF GFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF IAGKDRKTRN VFQIIKDAPD VALQAIELRK NALEIVRATG G RPIHPTSS ...String:
MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHHL AAAKAVDACF GFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF IAGKDRKTRN VFQIIKDAPD VALQAIELRK NALEIVRATG G RPIHPTSS TPGGISTELD DETQKDLLQK AQRNVELAEA TLELAVPIFE ENIDLVNSLG NIETYHTGLV KNGVWDVYDG IV RIKDKEG NLFREFKPAD YADTIAEHVK PYSWLKFPYI KDLGYPDGVY RVSPLSRLNV ADKMPDAAPK AQDYFKEFQD KFG YAQQTL LYHWARLIEV LACAECAADA LEGDLSGEKF PDSLERQAGD GVGIVEAPRG TLTHHYTCDE NGLITKANIV VATI QNNPA MEMGIQKVAQ DYIKPGVEVD DKIFNLMEMV IRAYDPCLSC ATHTIDSQMR LATLEVYDSE GDLVKRI

UniProtKB: F420-non-reducing hydrogenase subunit A

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 11 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #9: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 9 / Number of copies: 2 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

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Macromolecule #10: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #11: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

MacromoleculeName: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / type: ligand / ID: 11 / Number of copies: 1 / Formula: NFU
Molecular weightTheoretical: 195.591 Da
Chemical component information

ChemComp-NFU:
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

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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

MicroscopeTFS 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Particles had been C2 expanded / Number images used: 14332
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

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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
Output model

PDB-9sw3:
Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)

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