[English] 日本語
Yorodumi
- EMDB-53358: Structure of the energy converting methyltransferase (Mtr) of Met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53358
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Map dataLocal refinement MtrH
Sample
  • Complex: Mtr complex
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit B
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit F
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit H
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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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

-
Structure visualization

Supplemental images

emd_53358.png

Downloads & links

-
Map

FileDownload / File: emd_53358.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement MtrH
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: 0.16
Minimum - Maximum-0.5531261 - 0.86833495
Average (Standard dev.)0.00031656868 (±0.014620557)
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 1 local refinement MtrH

Fileemd_53358_half_map_1.map
AnnotationHalf map 1 local refinement MtrH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 local refinement MtrH

Fileemd_53358_half_map_2.map
AnnotationHalf map 2 local refinement MtrH
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 B
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit F
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit H

-
Supramolecule #1: Mtr complex

SupramoleculeName: Mtr complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: model of MtrH dimer, MtrB N-terminal sheets, MtrF N-terminal helical segment
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)

-
Macromolecule #1: Tetrahydromethanopterin S-methyltransferase subunit B

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit B / 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: 11.87963 KDa
SequenceString:
MSIVRIAPEI NLVMDTESGT VTQERKDSIQ YSMEPVFERV DKLDAIADDL VNSLSPSKPL LNTWPGRENT SYIAGIYSNS FYGIIVGLA FSGLLALIIY ITRLMGGVV

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit B

-
Macromolecule #2: Tetrahydromethanopterin S-methyltransferase subunit F

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit F / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 7.573959 KDa
SequenceString:
MAEEHEKGVP MVLAPQMGAI DATVESIRYR AQLIARNQKL DSGVAATGII GFAAGFLFSL LMVIVLPVAV GL

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit F

-
Macromolecule #3: Tetrahydromethanopterin S-methyltransferase subunit H

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit H / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: tetrahydromethanopterin S-methyltransferase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 34.07573 KDa
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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: 3.2 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