[English] 日本語
Yorodumi
- EMDB-53360: Structure of the energy converting methyltransferase (Mtr) of Met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53360
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Map datalocal refinement of MtrA/i
Sample
  • Complex: Mtr complex
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit A
    • Protein or peptide: Conserved protein
  • Ligand: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
KeywordsSodium-pumping / membrane-bound / methyltransferase complex / methanogen / methanogenic / methylotrophic / archaeon / archaea / methanosarcina / methanosarcina mazei / Vitamin B12 / corrinoid / cobalt / 5-hydroxybenzimidazole / small protein / oxygen-sensitive / MEMBRANE PROTEIN
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methanogenesis, from carbon dioxide / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
Tetrahydromethanopterin S-methyltransferase subunit A / Conserved protein
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsReif-Trauttmansdorff T / Herdering E / Bohn S / Pascoa TC / Kumar A / Zimmer E / Schmitz RA / Schuller JM
Funding supportEuropean Union, 1 items
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, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53360.png

Downloads & links

-
Map

FileDownload / File: emd_53360.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement of MtrA/i
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 576 pix.
= 417.6 Å		0.73 Å/pix.
x 576 pix.
= 417.6 Å		0.73 Å/pix.
x 576 pix.
= 417.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3725542 - 0.58714324
Average (Standard dev.)0.00014764891 (±0.008156843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 417.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A local refinement of MtrA/i

Fileemd_53360_half_map_1.map
Annotationhalf map A local refinement of MtrA/i
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B local refinement of MtrA/i

Fileemd_53360_half_map_2.map
Annotationhalf map B local refinement of MtrA/i
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mtr complex

EntireName: Mtr complex
Components
  • Complex: Mtr complex
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit A
    • Protein or peptide: Conserved protein
  • Ligand: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE

-
Supramolecule #1: Mtr complex

SupramoleculeName: Mtr complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)

-
Macromolecule #1: Tetrahydromethanopterin S-methyltransferase subunit A

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 25.395191 KDa
SequenceString: MADKREPAPG WPILKGEYEV GDVKNSVLVI TCGSHLPGKP ILDAGAACTG SCKTENLGIE KVVAHIISNP NIRYLLVTGS EVKGHITGQ SMMSLHANGV KENRIAGALG AIPYVENLNA AAVARFQEQV QVVNLLDTED MGAITSKVRE LASKDPGAFD A DPLVVEIS ...String:
MADKREPAPG WPILKGEYEV GDVKNSVLVI TCGSHLPGKP ILDAGAACTG SCKTENLGIE KVVAHIISNP NIRYLLVTGS EVKGHITGQ SMMSLHANGV KENRIAGALG AIPYVENLNA AAVARFQEQV QVVNLLDTED MGAITSKVRE LASKDPGAFD A DPLVVEIS EEGEEEEEGG VVRPVSGEIA VLRSRLKAIE ARMMDIGNLN KFHSGVHAGK VEGAMIGLTI TISLLGLLLL GR

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit A

-
Macromolecule #2: Conserved protein

MacromoleculeName: Conserved protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 7.623597 KDa
SequenceString:
MKCEACGRES DTKYCNDCGK VMDEVVRRVG EARWAAIDDC SFIYPLVQRV GRGEATVNDI IQALDVED

UniProtKB: Conserved protein

-
Macromolecule #3: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE

MacromoleculeName: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: B13
Molecular weightTheoretical: 1.321326 KDa
Chemical component information

ChemComp-B13:
5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10.0 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136531
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more