9SW5 | pdb_00009sw5

Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 1 substate b (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9SW5/pdb
EM Map EMD-55298: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Methanothermobacter marburgensis
Mutation(s): No

Deposited: 2025-10-04 Released: 2026-04-29
Deposition Author(s): San Segundo-Acosta, P., Murphy, B.J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens

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

(2026) Science Advances

Macromolecule Content

Total Structure Weight: 234.68 kDa
Atom Count: 15,670
Modeled Residue Count: 2,004
Deposited Residue Count: 2,067
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A	A	659	Methanothermobacter marburgensis	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50756
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B	B	302	Methanothermobacter marburgensis	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50755
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C	C	185	Methanothermobacter marburgensis	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50754
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase subunit A	D [auth F]	472	Methanothermobacter marburgensis	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60227
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase subunit G	E	308	Methanothermobacter marburgensis	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60239
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase iron-sulfur subunit D	F [auth D]	141	Methanothermobacter marburgensis	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60238
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
9S8 (Subject of Investigation/LOI) Query on 9S8 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	N [auth B], O [auth B]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain H [auth A]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E]
NFU (Subject of Investigation/LOI) Query on NFU Download:Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]