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- EMDB-53360: Structure of the energy converting methyltransferase (Mtr) of Met... -

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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: Reif-Trauttmansdorff T / Herdering E / Bohn S / Pascoa TC / Kumar A / Zimmer E / Schmitz RA / Schuller JM
History
DepositionApr 9, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53360.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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Sample components

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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

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Supramolecule #1: Mtr complex

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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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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)

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