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 9SW3 | pdb_00009sw3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history. 

Literature

Diversity of electron-bifurcating CO 2 -fixing supercomplexes in methanogens.

Segundo-Acosta, P.S., Nomura, S., Fernandes-Queiroz, J.P., Protasov, E., Kahnt, J., Kaneko, M., Hochberg, G., Shima, S., Murphy, B.J.

(2026) Sci Adv 12: eaed3711-eaed3711

  • DOI: https://doi.org/10.1126/sciadv.aed3711
  • Primary Citation Related Structures: 
    9SW2, 9SW3, 9SW4, 9SW5, 9SW6

  • PubMed Abstract: 

    In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO 2 , 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) 2 -Fmd 4 supercomplex from a Class I methanogen, Methanothermobacter marburgensis , 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.


  • Organizational Affiliation: 
    • Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 234.68 kDa 
  • Atom Count: 15,643 
  • Modeled Residue Count: 2,002 
  • Deposited Residue Count: 2,067 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A659Methanothermobacter marburgensisMutation(s): 0 
EC: 1.8.98.5
UniProt
Find proteins for Q50756 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore Q50756 
Go to UniProtKB:  Q50756
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50756
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B302Methanothermobacter marburgensisMutation(s): 0 
EC: 1.8.98.5
UniProt
Find proteins for Q50755 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore Q50755 
Go to UniProtKB:  Q50755
Entity Groups
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UniProt GroupQ50755
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C185Methanothermobacter marburgensisMutation(s): 0 
EC: 1.8.98.5
UniProt
Find proteins for Q50754 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore Q50754 
Go to UniProtKB:  Q50754
Entity Groups
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UniProt GroupQ50754
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase iron-sulfur subunit D141Methanothermobacter marburgensisMutation(s): 0 
EC: 1.12.99
UniProt
Find proteins for P60238 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P60238 
Go to UniProtKB:  P60238
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UniProt GroupP60238
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase subunit G308Methanothermobacter marburgensisMutation(s): 0 
EC: 1.12.99
UniProt
Find proteins for P60239 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P60239 
Go to UniProtKB:  P60239
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UniProt GroupP60239
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase subunit A472Methanothermobacter marburgensisMutation(s): 0 
EC: 1.12.99
UniProt
Find proteins for P60227 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P60227 
Go to UniProtKB:  P60227
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UniProt GroupP60227
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
J [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
9S8
(Subject of Investigation/LOI)

Query on 9S8



Download:Ideal Coordinates CCD File
N [auth B],
O [auth B]
Non-cubane [4Fe-4S]-cluster
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
K [auth A]
L [auth A]
G [auth A],
H [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A],
P [auth C],
Q [auth C],
S [auth E],
T [auth E],
U [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
R [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FCO
(Subject of Investigation/LOI)

Query on FCO



Download:Ideal Coordinates CCD File
V [auth F]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI
(Subject of Investigation/LOI)

Query on NI



Download:Ideal Coordinates CCD File
W [auth F]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-29
    Type: Initial release
  • Version 2.0: 2026-09-23
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-09-30
    Changes: Data collection, Database references