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- PDB-9sw6: Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marbu... -

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Entry
Database: PDB / ID: 9sw6
TitleStructure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)
Components
  • (F420-non-reducing hydrogenase subunit ...) x 2
  • (H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ...) x 3
  • (Tungsten formylmethanofuran dehydrogenase, subunit ...) x 3
  • F420-non-reducing hydrogenase iron-sulfur subunit D
  • Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
  • Polyferredoxin protein MvhB
  • formylmethanofuran dehydrogenase subunit B
KeywordsOXIDOREDUCTASE / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / methanogenesis, from carbon dioxide / CoB--CoM heterodisulfide reductase activity / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / methanogenesis, from carbon dioxide / CoB--CoM heterodisulfide reductase activity / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding / ferredoxin hydrogenase activity / molybdopterin cofactor binding / nickel cation binding / iron-sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Formylmethanofuran dehydrogenase, fused subunit C/D / 4Fe-4S binding domain / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C ...Formylmethanofuran dehydrogenase, fused subunit C/D / 4Fe-4S binding domain / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : / 3Fe-4S ferredoxin / Glutamate synthase, alpha subunit, C-terminal domain superfamily / : / 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 / Amidohydrolase 3 / Amidohydrolase family / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / 4Fe-4S dicluster domain / 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 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Metal-dependent hydrolase, composite domain superfamily / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / Chem-MGD / MOLYBDENUM ATOM / Chem-NFU / IRON/SULFUR CLUSTER / Tungsten formylmethanofuran dehydrogenase, subunit F ...Non-cubane [4Fe-4S]-cluster / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / Chem-MGD / MOLYBDENUM ATOM / Chem-NFU / IRON/SULFUR CLUSTER / Tungsten formylmethanofuran dehydrogenase, subunit F / Tungsten formylmethanofuran dehydrogenase, subunit G / Tungsten formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B / F420-non-reducing hydrogenase subunit A / Polyferredoxin protein MvhB / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSan Segundo-Acosta, P. / Murphy, B.J.
Funding support Germany, 1items
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, J.P. / Protasov, E. / Kahnt, J. / Kaneko, M. / Hochberg, G. / Shima, S. / Murphy, B.J.
History
DepositionOct 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
D: F420-non-reducing hydrogenase iron-sulfur subunit D
E: F420-non-reducing hydrogenase subunit G
H: Tungsten formylmethanofuran dehydrogenase, subunit F
I: Tungsten formylmethanofuran dehydrogenase, subunit A
J: formylmethanofuran dehydrogenase subunit B
L: Tungsten formylmethanofuran dehydrogenase, subunit G
i: Tungsten formylmethanofuran dehydrogenase, subunit A
l: Tungsten formylmethanofuran dehydrogenase, subunit G
j: formylmethanofuran dehydrogenase subunit B
K: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
h: Tungsten formylmethanofuran dehydrogenase, subunit F
k: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
G: Polyferredoxin protein MvhB
F: F420-non-reducing hydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)697,99980
Polymers676,53517
Non-polymers21,46463
Water6,179343
1
A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
D: F420-non-reducing hydrogenase iron-sulfur subunit D
E: F420-non-reducing hydrogenase subunit G
H: Tungsten formylmethanofuran dehydrogenase, subunit F
I: Tungsten formylmethanofuran dehydrogenase, subunit A
J: formylmethanofuran dehydrogenase subunit B
L: Tungsten formylmethanofuran dehydrogenase, subunit G
i: Tungsten formylmethanofuran dehydrogenase, subunit A
l: Tungsten formylmethanofuran dehydrogenase, subunit G
j: formylmethanofuran dehydrogenase subunit B
K: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
h: Tungsten formylmethanofuran dehydrogenase, subunit F
k: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
G: Polyferredoxin protein MvhB
F: F420-non-reducing hydrogenase subunit A
hetero molecules

A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
D: F420-non-reducing hydrogenase iron-sulfur subunit D
E: F420-non-reducing hydrogenase subunit G
H: Tungsten formylmethanofuran dehydrogenase, subunit F
I: Tungsten formylmethanofuran dehydrogenase, subunit A
J: formylmethanofuran dehydrogenase subunit B
L: Tungsten formylmethanofuran dehydrogenase, subunit G
i: Tungsten formylmethanofuran dehydrogenase, subunit A
l: Tungsten formylmethanofuran dehydrogenase, subunit G
j: formylmethanofuran dehydrogenase subunit B
K: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
h: Tungsten formylmethanofuran dehydrogenase, subunit F
k: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
G: Polyferredoxin protein MvhB
F: F420-non-reducing hydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,395,998160
Polymers1,353,07034
Non-polymers42,927126
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

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H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ... , 3 types, 3 molecules ABC

#1: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A / CoB--CoM heterodisulfide reductase iron-sulfur subunit A


Mass: 72264.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50756, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#2: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / CoB--CoM heterodisulfide reductase subunit B


Mass: 33496.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50755, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#3: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / CoB--CoM heterodisulfide reductase iron-sulfur subunit C


Mass: 20548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50754, H2:CoB-CoM heterodisulfide,ferredoxin reductase

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Protein , 4 types, 6 molecules DJjKkG

#4: Protein F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl viologen-reducing hydrogenase subunit delta / MVH subunit D


Mass: 15954.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60238, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
#8: Protein formylmethanofuran dehydrogenase subunit B


Mass: 48179.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PXE7, formylmethanofuran dehydrogenase
#10: Protein Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C / Molybdenum-containing formylmethanofuran dehydrogenase I subunit C


Mass: 43383.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P61937, formylmethanofuran dehydrogenase
#11: Protein Polyferredoxin protein MvhB


Mass: 44090.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60232

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F420-non-reducing hydrogenase subunit ... , 2 types, 2 molecules EF

#5: Protein F420-non-reducing hydrogenase subunit G / Methyl viologen-reducing hydrogenase subunit gamma / MVH subunit G


Mass: 33786.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60239, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
#12: Protein F420-non-reducing hydrogenase subunit A / Methyl viologen-reducing hydrogenase subunit alpha / MVH subunit A


Mass: 52905.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60227, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors

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Tungsten formylmethanofuran dehydrogenase, subunit ... , 3 types, 6 molecules HhIiLl

#6: Protein Tungsten formylmethanofuran dehydrogenase, subunit F


Mass: 38614.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PU51, formylmethanofuran dehydrogenase
#7: Protein Tungsten formylmethanofuran dehydrogenase, subunit A


Mass: 63001.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PU54, formylmethanofuran dehydrogenase
#9: Protein Tungsten formylmethanofuran dehydrogenase, subunit G


Mass: 8564.948 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PU52, formylmethanofuran dehydrogenase

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Non-polymers , 11 types, 406 molecules

#13: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#15: Chemical ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HFeN2NiO / Feature type: SUBJECT OF INVESTIGATION
#23: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Buffer solutionpH: 7.6
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.55 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 18777
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10RELIONinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 917008
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 722594
Details: Particles had been C2-symmetry expanded. It is a composite map
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Generated using ModelAngelo / Source name: Other / Type: other
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00262063
ELECTRON MICROSCOPYf_angle_d0.50384669
ELECTRON MICROSCOPYf_dihedral_angle_d4.948386
ELECTRON MICROSCOPYf_chiral_restr0.0439624
ELECTRON MICROSCOPYf_plane_restr0.00410797

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