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- PDB-9qtp: Structure of the energy converting methyltransferase (Mtr) of Met... -

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Basic information

Entry
Database: PDB / ID: 9qtp
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Components
  • Tetrahydromethanopterin S-methyltransferase subunit B
  • Tetrahydromethanopterin S-methyltransferase subunit F
  • Tetrahydromethanopterin S-methyltransferase subunit H
KeywordsMEMBRANE PROTEIN / Sodium-pumping / membrane-bound / methyltransferase complex / methanogen / methanogenic / methylotrophic / archaeon / archaea / methanosarcina / methanosarcina mazei / Vitamin B12 / corrinoid / cobalt / 5-hydroxybenzimidazole / small protein / oxygen-sensitive
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF) / Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Dihydropteroate synthase-like
Similarity search - Domain/homology
Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase subunit F / Tetrahydromethanopterin S-methyltransferase subunit B
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsReif-Trauttmansdorff, T. / Herdering, E. / Bohn, S. / Pascoa, T.C. / Kumar, A. / Zimmer, E. / Schmitz, R.A. / Schuller, J.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI.
Authors: Tristan Reif-Trauttmansdorff / Eva Herdering / Stefan Bohn / Tomas Pascoa / Jörg Kahnt / Erik Zimmer / Anuj Kumar / Ruth A Schmitz / Jan M Schuller /
Abstract: Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase ...Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase complex: the N⁵-tetrahydromethanopterin:CoM-S-methyltransferase (Mtr). It couples methyl transfer between two methanogen-specific cofactors with sodium ion transport across the membrane, forming the only energy-conserving step in hydrogenotrophic methanogenesis. Here, we present a 2.1 Å single-particle cryo-EM structure of the Mtr complex from Methanosarcina mazei. The structure reveals the organization of all catalytic subunits, embedded archaeal lipids and the sodium-binding site. Most strikingly, we discover MtrI, a previously unannotated small open-reading frame encoded protein ( < 100 aa) found within the order of Methanosarcinales that binds both the top of the sodium-channel and cytosolic domain of MtrA via its cobamide cofactor in response to oxygen exposure. This interaction likely prevents sodium leakage and stabilizes the complex under oxidative conditions, revealing an unexpected regulatory mechanism in methanogen energy conservation.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Tetrahydromethanopterin S-methyltransferase subunit B
P: Tetrahydromethanopterin S-methyltransferase subunit F
o: Tetrahydromethanopterin S-methyltransferase subunit H
p: Tetrahydromethanopterin S-methyltransferase subunit H


Theoretical massNumber of molelcules
Total (without water)87,6054
Polymers87,6054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit B / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit B


Mass: 11879.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina mazei Go1 (archaea)
References: UniProt: P80655, tetrahydromethanopterin S-methyltransferase
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit F / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit F


Mass: 7573.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina mazei Go1 (archaea)
References: UniProt: P80654, tetrahydromethanopterin S-methyltransferase
#3: Protein Tetrahydromethanopterin S-methyltransferase subunit H / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit H


Mass: 34075.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina mazei Go1 (archaea)
References: UniProt: P80650, tetrahydromethanopterin S-methyltransferase
Has protein modificationN

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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: Mtr complex / Type: COMPLEX
Details: model of MtrH dimer, MtrB N-terminal sheets, MtrF N-terminal helical segment
Entity ID: all / Source: NATURAL
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136531 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00335180
ELECTRON MICROSCOPYf_angle_d0.54847033
ELECTRON MICROSCOPYf_chiral_restr0.045809
ELECTRON MICROSCOPYf_plane_restr0.0048912
ELECTRON MICROSCOPYf_dihedral_angle_d7.5649721

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