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- PDB-9sw3: Structure of the MvhAGD-HdrABC dimer of M. marburgensis under sta... -

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Entry
Database: PDB / ID: 9sw3
TitleStructure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)
Components
  • (F420-non-reducing hydrogenase subunit ...) x 2
  • (H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ...) x 3
  • F420-non-reducing hydrogenase iron-sulfur subunit D
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 / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit B / : / CoB--CoM heterodisulphide reductase, subunit C / Cysteine-rich domain / Cysteine-rich domain / F420-non-reducing hydrogenase iron-sulfur subunit D / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like ...: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit B / : / CoB--CoM heterodisulphide reductase, subunit C / Cysteine-rich domain / Cysteine-rich domain / F420-non-reducing hydrogenase iron-sulfur subunit D / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / HoxL-like / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / 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
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / CARBONMONOXIDE-(DICYANO) IRON / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / IRON/SULFUR CLUSTER / 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 ...Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / CARBONMONOXIDE-(DICYANO) IRON / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / IRON/SULFUR CLUSTER / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsSan Segundo-Acosta, P. / Murphy, B.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2026
Title: Diversity of electron-bifurcating CO-fixing supercomplexes in methanogens.
Authors: Pablo San Segundo-Acosta / Shunsuke Nomura / Joao Pedro Fernandes-Queiroz / Evgenii Protasov / Jörg Kahnt / Masanori Kaneko / Georg Hochberg / Seigo Shima / Bonnie J Murphy /
Abstract: In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO, driven by low-potential electrons provided by electron-bifurcating heterodisulfide reductase ...In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO, driven by low-potential electrons provided by electron-bifurcating heterodisulfide reductase (Hdr) complexed with electron-donating proteins such as Mvh hydrogenase. Here, we report the structure of a C2-symmetric (Mvh-Hdr)-Fmd supercomplex from a Class I methanogen, , which is architecturally different from the previously reported ring-shaped D3-symmetric supercomplex of a methanogen belonging to phylogenetically distinct Class II methanogens. In this C2-symmetric form, the redox active sites of Hdr and Fmd are connected by two MvhB polyferredoxins, whose branching electron paths appear to be available for electron transfer to/from other partners. The ancestral form was likely C2 symmetric, whereas D3-symmetric supercomplexes were acquired by horizontal gene transfer, a transition probably helpful for growth in substrate-poor environments.
History
DepositionOct 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation
Revision 1.1Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Structure summary / Data content type: EM metadata / EM metadata / Category: em_admin / entity / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
F: F420-non-reducing hydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,68323
Polymers228,9566
Non-polymers5,72717
Water00
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
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
F: F420-non-reducing hydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,36746
Polymers457,91212
Non-polymers11,45534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodUCSF CHIMERA

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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 , 1 types, 1 molecules D

#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

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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
#6: 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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Non-polymers , 6 types, 17 molecules

#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#9: 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
#10: 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
#11: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION

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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: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
Type: COMPLEX / Entity ID: #1, #4-#5, #2-#3, #6 / 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14332 / Algorithm: FOURIER SPACE / Details: Particles had been C2 expanded / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Generated using ModelAngelo / Source name: Other / Type: other
RefinementHighest resolution: 3.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223220
ELECTRON MICROSCOPYf_angle_d0.48631549
ELECTRON MICROSCOPYf_dihedral_angle_d4.1583128
ELECTRON MICROSCOPYf_chiral_restr0.0413532
ELECTRON MICROSCOPYf_plane_restr0.0034053

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