9T1S | pdb_00009t1s

Heterodisulfide-Hydrogenase-Formate Dehydrogenase dimer

PDB DOI: https://doi.org/10.2210/pdb9T1S/pdb
EM Map EMD-55451: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Methanococcus maripaludis
Mutation(s): No

Deposited: 2025-10-22 Released: 2026-07-01
Deposition Author(s): Paul, S., Schuller, J.M.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Architecture of the 8 MDa Hdr-Vhu-Fwd super-assembly in class I methanogens.

Paul, S., Pascoa, T.C., Klamke, M.A., Bohn, S., Abendroth, F., Deobald, D., Vazquez, O., Stripp, S.T., Schuller, J.M.

(2026) Nature

PubMed: 42420451 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-026-10744-9
Primary Citation Related Structures:
9SFI, 9T1S

PubMed Abstract:
Methanogens are central to global carbon cycling and among the largest biological sources of methane, a potent greenhouse gas ¹. At the heart of their energy metabolism lies the Hdr-Vhu-Fwd super-assembly, which couples H ₂ oxidation with CO ₂ reduction through flavin-based electron bifurcation. Here we present the cryogenic electron microscopy structure of the Hdr-Vhu-Fwd super-assembly from Methanococcus maripaludis, revealing an 8 MDa complex comprising 252 polypeptide chains and over 600 redox cofactors. Cryo-electron tomography further support that this super-assembly forms an intact structure within the cytoplasm of intact cells. This architecture comprises two hexameric HdrABC-Vhu rings linked by a tetrameric FwdF core, forming a continuous, circular electron chain. In this unique arrangement, 12 polyferredoxin subunits (VhuB) connect the Vhu-Hdr and Fwd complexes, thereby coupling electron bifurcation with CO ₂ reduction and directly linking the last and the first step of methanogenesis. Moreover, we identify a modular variant of the complex in which the [NiFe]-hydrogenase Vhu is substituted by tungsten-containing formate dehydrogenase (FdhAB), indicating flexible integration of electron-input modules facilitating metabolic adaptation under diverse environmental conditions ². Analysis of the taxonomic distribution reveals that this architecture is specific to class I methanogens and is distinct from the smaller Hdr-Fmd complex of class II ³. Together, our study reveals that the the Hdr-Vhu-Fwd super-assembly has a modular and adaptable bioenergetic assembly, suggesting a lineage-specific architecture to adapt to diverse anaerobic niches.

Organizational Affiliation

Department of Chemistry and Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 488.28 kDa
Atom Count: 33,539
Modeled Residue Count: 4,328
Deposited Residue Count: 4,328
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CoB--CoM heterodisulfide reductase iron-sulfur subunit A	A, B	658	Methanococcus maripaludis	Mutation(s): 0 EC: 1.8
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase subunit B	C, D	293	Methanococcus maripaludis	Mutation(s): 0 EC: 1.8.98.1
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2	E, F	184	Methanococcus maripaludis	Mutation(s): 0 EC: 1.8.98.5 (PDB Primary Data), 1.8.98.6 (PDB Primary Data)
UniProt
Find proteins for Q6LYD7 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LYD7 Go to UniProtKB: Q6LYD7
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UniProt Group	Q6LYD7
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420-reducing hydrogenase, alpha subunit	G	418	Methanococcus maripaludis	Mutation(s): 0 EC: 1.12.1.2 (PDB Primary Data), 1.12.99 (PDB Primary Data)
UniProt
Find proteins for A0A2L1CAX5 (Methanococcus maripaludis) Explore A0A2L1CAX5 Go to UniProtKB: A0A2L1CAX5
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UniProt Group	A0A2L1CAX5
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase small subunit	H	288	Methanococcus maripaludis	Mutation(s): 0 EC: 1.12.99
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase subunit delta	I, J	134	Methanococcus maripaludis	Mutation(s): 0
UniProt
Find proteins for A0A2L1CBC1 (Methanococcus maripaludis) Explore A0A2L1CBC1 Go to UniProtKB: A0A2L1CBC1
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UniProt Group	A0A2L1CBC1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
F420 non-reducing hydrogenase subunit	K	27	Methanococcus maripaludis	Mutation(s): 0
UniProt
Find proteins for A0A2L1CB29 (Methanococcus maripaludis) Explore A0A2L1CB29 Go to UniProtKB: A0A2L1CB29
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UniProt Group	A0A2L1CB29
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
formate dehydrogenase (coenzyme F420)	L	674	Methanococcus maripaludis	Mutation(s): 0 EC: 1.17.98.3
UniProt
Find proteins for M9QXF8 (Methanococcus maripaludis) Explore M9QXF8 Go to UniProtKB: M9QXF8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M9QXF8
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
formate dehydrogenase (coenzyme F420)	M	383	Methanococcus maripaludis	Mutation(s): 0 EC: 1.17.98.3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

Small Molecules

Ligands 7 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 Q [auth A] SDF format, chain XA [auth M] SDF format, chain X [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain XA [auth M] MOL2 format, chain X [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain XA [auth M] mmCIF format, chain X [auth B]	Q [auth A], X [auth B], XA [auth M]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain Q [auth A] Focus chain X [auth B] Focus chain XA [auth M] Interactions & Density Focus chain Q [auth A] Focus chain X [auth B] Focus chain XA [auth M]
MGD (Subject of Investigation/LOI) Query on MGD Download:Ideal Coordinates CCD File SDF format, chain RA [auth L] SDF format, chain SA [auth L] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth L] mmCIF format, chain RA [auth L] mmCIF format, chain SA [auth L]	RA [auth L], SA [auth L]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain RA [auth L] Focus chain SA [auth L] Interactions & Density Focus chain RA [auth L] Focus chain SA [auth L]
9S8 (Subject of Investigation/LOI) Query on 9S8 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D]	BA [auth C], CA [auth C], DA [auth D], EA [auth D]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth L] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth M] SDF format, chain U [auth B] SDF format, chain UA [auth M] SDF format, chain V [auth B] SDF format, chain VA [auth M] SDF format, chain W [auth B] SDF format, chain WA [auth M] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth L] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth M] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth M] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth M] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth M] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth L] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth M] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth M] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth M] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth M] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] FA [auth E] GA [auth E] HA [auth F] IA [auth F] AA [auth B], FA [auth E], GA [auth E], HA [auth F], IA [auth F], KA [auth H], LA [auth H], MA [auth H], N [auth A], O [auth A], P [auth A], PA [auth L], R [auth A], S [auth A], T [auth A], TA [auth M], U [auth B], UA [auth M], V [auth B], VA [auth M], W [auth B], WA [auth M], Y [auth B], Z [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth L] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth M] Focus chain U [auth B] Focus chain UA [auth M] Focus chain V [auth B] Focus chain VA [auth M] Focus chain W [auth B] Focus chain WA [auth M] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth L] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth M] Focus chain U [auth B] Focus chain UA [auth M] Focus chain V [auth B] Focus chain VA [auth M] Focus chain W [auth B] Focus chain WA [auth M] Focus chain Y [auth B] Focus chain Z [auth B]
NFU (Subject of Investigation/LOI) Query on NFU Download:Ideal Coordinates CCD File SDF format, chain JA [auth G] MOL2 format, chain JA [auth G] mmCIF format, chain JA [auth G]	JA [auth G]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ Fe N₂ Ni O DMIYQIPDCONFNN-UHFFFAOYSA-N		Interactions Focus chain JA [auth G] Interactions & Density Focus chain JA [auth G]
W (Subject of Investigation/LOI) Query on W Download:Ideal Coordinates CCD File SDF format, chain QA [auth L] MOL2 format, chain QA [auth L] mmCIF format, chain QA [auth L]	QA [auth L]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain QA [auth L] Interactions & Density Focus chain QA [auth L]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain NA [auth I] SDF format, chain OA [auth J] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth J] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth J]	NA [auth I], OA [auth J]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain NA [auth I] Focus chain OA [auth J] Interactions & Density Focus chain NA [auth I] Focus chain OA [auth J]