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- EMDB-53359: Structure of the energy converting methyltransferase (Mtr) of Met... -

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Basic information

Entry
Database: EMDB / ID: EMD-53359
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Map dataNU-refinement of Mtr, consensus-map
Sample
  • Complex: Mtr complex
    • Protein or peptide: x 7 types
  • Ligand: x 6 types
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 / vesicle membrane / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane / cytoplasm
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F ...Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit C / 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 A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit A / Tetrahydromethanopterin S-methyltransferase subunit E / Tetrahydromethanopterin S-methyltransferase subunit D / Tetrahydromethanopterin S-methyltransferase subunit F / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase subunit G
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 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

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Structure visualization

Supplemental images

emd_53359.png

Downloads & links

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Map

FileDownload / File: emd_53359.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNU-refinement of Mtr, consensus-map
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: 0.09
Minimum - Maximum-0.26057816 - 0.54010373
Average (Standard dev.)0.00014512619 (±0.011119479)
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 B of NU-refinement of Mtr, consensus-map

Fileemd_53359_half_map_1.map
AnnotationHalf map B of NU-refinement of Mtr, consensus-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of NU-refinement of Mtr, consensus-map

Fileemd_53359_half_map_2.map
AnnotationHalf map A of NU-refinement of Mtr, consensus-map
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: Tetrahydromethanopterin S-methyltransferase subunit B
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit C
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit D
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit E
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit F
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit G
  • Ligand: 2-Hydroxy-archaetidylinositol
  • Ligand: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
  • Ligand: Archaetidylinositol
  • Ligand: SODIUM ION
  • Ligand: Archaetidylethanolamine
  • Ligand: water

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Supramolecule #1: Mtr complex

SupramoleculeName: Mtr complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
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: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 25.395191 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
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: Tetrahydromethanopterin S-methyltransferase subunit B

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 11.87963 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString:
MSIVRIAPEI NLVMDTESGT VTQERKDSIQ YSMEPVFERV DKLDAIADDL VNSLSPSKPL LNTWPGRENT SYIAGIYSNS FYGIIVGLA FSGLLALIIY ITRLMGGVV

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit B

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Macromolecule #3: Tetrahydromethanopterin S-methyltransferase subunit C

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 26.953893 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString: MSAGGAGGEA KGAYPQQTLM ALGIVGGLVG IYLGHFMPPA YSFFGGIGAI CATVWGADAV RRVASYGLGT GVPSIGMLAL GMGILAALF GLALGGIAGP ILAVVVAAII GGVIGALANK VIGMGIPIME QAMIEISCAG TLVILGLSVV IAGSFDYAAI I ENVIANGY ...String:
MSAGGAGGEA KGAYPQQTLM ALGIVGGLVG IYLGHFMPPA YSFFGGIGAI CATVWGADAV RRVASYGLGT GVPSIGMLAL GMGILAALF GLALGGIAGP ILAVVVAAII GGVIGALANK VIGMGIPIME QAMIEISCAG TLVILGLSVV IAGSFDYAAI I ENVIANGY IALIFIIGGM GILHPFNACL GPDESQDRTL ILAVEKAAIA LIITGFASSL HEGLMTAGIN ILVGLVIWYV AF SKYYALI KRDAYAVVGT GLLPSAEELQ

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit C

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Macromolecule #4: Tetrahydromethanopterin S-methyltransferase subunit D

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 25.279777 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString: MIDAILGNIL WMVFIIIGGV LISWGVHFVP VGGAPAAMAQ ATGVGTGTVQ LATGAGLTGL VSAGFMMNVT DNFPLIVASG AVGAMIMIA VTMIVGTWIY VYGVGCVPSS AKVKVDPITK YRQDLYVSQG TEGHGIPTVS FVSGVIGAAL GGIGGSLIYY S LIEVGVSV ...String:
MIDAILGNIL WMVFIIIGGV LISWGVHFVP VGGAPAAMAQ ATGVGTGTVQ LATGAGLTGL VSAGFMMNVT DNFPLIVASG AVGAMIMIA VTMIVGTWIY VYGVGCVPSS AKVKVDPITK YRQDLYVSQG TEGHGIPTVS FVSGVIGAAL GGIGGSLIYY S LIEVGVSV GLERVGVTSA VTGNSLVAVA AIFAIGIFLV NAVIPSYNIG GTIEGFHDPK FKKWPKAVIS SVVASILCAI VA VIAIAQL GGI

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit D

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Macromolecule #5: Tetrahydromethanopterin S-methyltransferase subunit E

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 35.539625 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString: MEPLIGMGVL ALIGVAATIA GASEDLESDI GSQSNPNSQV QLAPQMMFPH RIFNKAISGE PPSNALMCSI GAAIATVLIS EFTVSPLFA LVFGSVIAAS VHATFAVTAT MGRCASQSRF KQPIYLDMIR SHTPAIMGYA FITTFCVLIV SYLMTVVLGH P FPLTMLAF ...String:
MEPLIGMGVL ALIGVAATIA GASEDLESDI GSQSNPNSQV QLAPQMMFPH RIFNKAISGE PPSNALMCSI GAAIATVLIS EFTVSPLFA LVFGSVIAAS VHATFAVTAT MGRCASQSRF KQPIYLDMIR SHTPAIMGYA FITTFCVLIV SYLMTVVLGH P FPLTMLAF IWGITIGAIG SSTGDVHYGA EREFQQFEFG SGLNASNSGN IVRYAESGLR NGFDNSWFCS KFGGPTTGIA FG MTVFLGS WITTIFDPAQ GLSMGWLSVI AGVIIVLILI IWNWKIEVQA RKAYGPYKED KAEEASASAW SHPQFEKGGG SGG GSGGSA WSHPQFEK

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit E

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Macromolecule #6: Tetrahydromethanopterin S-methyltransferase subunit F

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 7.573959 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString:
MAEEHEKGVP MVLAPQMGAI DATVESIRYR AQLIARNQKL DSGVAATGII GFAAGFLFSL LMVIVLPVAV GL

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit F

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Macromolecule #7: Tetrahydromethanopterin S-methyltransferase subunit G

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit G / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 8.030405 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString:
MDGKAPAAFV EPGEFNEVMK RLDQIDEKVE FVNSEVAQRI GKKVGRDIGI LYGGVIGLLL FLIYVQISSM FM

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit G

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Macromolecule #8: 2-Hydroxy-archaetidylinositol

MacromoleculeName: 2-Hydroxy-archaetidylinositol / type: ligand / ID: 8 / Number of copies: 6 / Formula: A1JAP
Molecular weightTheoretical: 836.214 Da

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Macromolecule #9: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL

MacromoleculeName: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / type: ligand / ID: 9 / Number of copies: 3 / Formula: L1P
Molecular weightTheoretical: 733.137 Da
Chemical component information

ChemComp-L1P:
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL

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Macromolecule #10: Archaetidylinositol

MacromoleculeName: Archaetidylinositol / type: ligand / ID: 10 / Number of copies: 3 / Formula: A1JAO
Molecular weightTheoretical: 911.277 Da

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Macromolecule #11: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 11 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #12: Archaetidylethanolamine

MacromoleculeName: Archaetidylethanolamine / type: ligand / ID: 12 / Number of copies: 3 / Formula: A1JAN
Molecular weightTheoretical: 776.205 Da

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 2640 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 136531
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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