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- EMDB-53361: Structure of the energy converting methyltransferase (Mtr) of Met... -

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Basic information

Entry
Database: EMDB / ID: EMD-53361
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Map datacomposite map of mtr from consensus and local map(s)
Sample
  • Complex: Mtr complex
    • Protein or peptide: x 9 types
  • Ligand: x 7 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 H / 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 H / 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 H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A / Dihydropteroate synthase-like
Similarity search - Domain/homology
Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit A / Tetrahydromethanopterin S-methyltransferase subunit H / 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 / Conserved protein
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: 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_53361.png

Downloads & links

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Map

FileDownload / File: emd_53361.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of mtr from consensus and local map(s)
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: 0.2
Minimum - Maximum0.12179239 - 0.5438392
Average (Standard dev.)0.16043046 (±0.0057005165)
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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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
    • Protein or peptide: Conserved protein
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit H
  • Ligand: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
  • 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-#9
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 / Details: c-terminal Twin-StrepTag / 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: Conserved protein

MacromoleculeName: Conserved protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 7.623597 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString:
MKCEACGRES DTKYCNDCGK VMDEVVRRVG EARWAAIDDC SFIYPLVQRV GRGEATVNDI IQALDVED

UniProtKB: Conserved protein

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Macromolecule #9: Tetrahydromethanopterin S-methyltransferase subunit H

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit H / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 34.07573 KDa
Recombinant expressionOrganism: Methanosarcina mazei Go1 (archaea)
SequenceString: MFKFDKKQEV FELGGVKFGG QPGENPTVLV STMFYARHKI VTDEDKGIFD RAAAETLWNT QVSLSDATGL PYVNQIVGET PESIKRYIE WFVGIDDRTP FLIDSSAGNV RAAAAQYCTE IGVADRAIHN SINASIEQSE IDVLTESDVS AAIVLAFNAT D PTVKGKID ...String:
MFKFDKKQEV FELGGVKFGG QPGENPTVLV STMFYARHKI VTDEDKGIFD RAAAETLWNT QVSLSDATGL PYVNQIVGET PESIKRYIE WFVGIDDRTP FLIDSSAGNV RAAAAQYCTE IGVADRAIHN SINASIEQSE IDVLTESDVS AAIVLAFNAT D PTVKGKID ILEVGGSGQT KGMLQVAKEC GIKYPIIDVA AMPLGAGSGA TIRSVPTLKG KFGLPIGGGY HNMASAWDWL RK FKKTQPD PKAIYMPTDI GTNLVAQIAG SDYLLYGPIE NVNQIFPAVA MVDIMLGETA KELGVEIADL ENHPVTKLT

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit H

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Macromolecule #10: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE

MacromoleculeName: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / type: ligand / ID: 10 / Number of copies: 1 / Formula: B13
Molecular weightTheoretical: 1.321326 KDa
Chemical component information

ChemComp-B13:
5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE

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Macromolecule #11: 2-Hydroxy-archaetidylinositol

MacromoleculeName: 2-Hydroxy-archaetidylinositol / type: ligand / ID: 11 / Number of copies: 6 / Formula: A1JAP
Molecular weightTheoretical: 836.214 Da

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Macromolecule #12: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL

MacromoleculeName: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / type: ligand / ID: 12 / 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 #13: Archaetidylinositol

MacromoleculeName: Archaetidylinositol / type: ligand / ID: 13 / Number of copies: 3 / Formula: A1JAO
Molecular weightTheoretical: 911.277 Da

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Macromolecule #14: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 14 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #15: Archaetidylethanolamine

MacromoleculeName: Archaetidylethanolamine / type: ligand / ID: 15 / Number of copies: 3 / Formula: A1JAN
Molecular weightTheoretical: 776.205 Da

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Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 2641 / 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: 150000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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