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- EMDB-18135: Cryo-EM structure of the methanogenic Na+ translocating N5-methyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-18135
TitleCryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex
Map data
Sample
  • Complex: Methyl-H4MPT:CoM methyltransferase
    • Protein or peptide: x 7 types
  • Ligand: x 4 types
Keywordsmethanogenesis / tetrahydromethanopterin / coenzyme M / vitamin B12 / Na+ transport / TRANSFERASE
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase activity / tetrahydromethanopterin S-methyltransferase / methyltransferase complex / methanogenesis, from carbon dioxide / vesicle membrane / sodium ion transport / 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 B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G ...Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / 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, 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 D / Tetrahydromethanopterin S-methyltransferase subunit A 1 / Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit E / Tetrahydromethanopterin S-methyltransferase subunit F / Tetrahydromethanopterin S-methyltransferase subunit G / Tetrahydromethanopterin S-methyltransferase subunit B
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsAziz I / Vonck J / Ermler U
Funding support Germany, 1 items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationGeorg Forster stipend Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis.
Authors: Iram Aziz / Kanwal Kayastha / Susann Kaltwasser / Janet Vonck / Sonja Welsch / Bonnie J Murphy / Jörg Kahnt / Di Wu / Tristan Wagner / Seigo Shima / Ulrich Ermler /
Abstract: Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy ...Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by -methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG) composed of the central Mtr(ABFG) stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B-carrying domain.
History
DepositionAug 4, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18135.png

Downloads & links

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Map

FileDownload / File: emd_18135.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03199677 - 0.09494891
Average (Standard dev.)0.00035324262 (±0.0028380791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18135_msk_1.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 : Methyl-H4MPT:CoM methyltransferase

EntireName: Methyl-H4MPT:CoM methyltransferase
Components
  • Complex: Methyl-H4MPT:CoM methyltransferase
    • Protein or peptide: Tetrahydromethanopterin S-methyltransferase subunit A 1
    • 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: MAGNESIUM ION
  • Ligand: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Methyl-H4MPT:CoM methyltransferase

SupramoleculeName: Methyl-H4MPT:CoM methyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 430 kDa/nm

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Macromolecule #1: Tetrahydromethanopterin S-methyltransferase subunit A 1

MacromoleculeName: Tetrahydromethanopterin S-methyltransferase subunit A 1
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 25.64032 KDa
SequenceString: MVEKKSPAEG WPVVNGDYIV GDPESPVAAT TLASHIEDIP VEAGAAIAGP CKTENLGIEK MIANLISNPN IRFLILCGSE VQGHITGQS IEALHQNGVD PDKRNIIGAT GAIPYIENIP DEGIERFQKQ LEIVNLIDVE DADAIKAKVK ECIEKDPGAF E EEAMIIKV ...String:
MVEKKSPAEG WPVVNGDYIV GDPESPVAAT TLASHIEDIP VEAGAAIAGP CKTENLGIEK MIANLISNPN IRFLILCGSE VQGHITGQS IEALHQNGVD PDKRNIIGAT GAIPYIENIP DEGIERFQKQ LEIVNLIDVE DADAIKAKVK ECIEKDPGAF E EEAMIIKV EEGGEEEEGE EVKPVAPETA LIEARMRNIQ TQVKMIGSTN RMFAGMYSGK VQGIMIGLAF TLTLGILLLV

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit A 1

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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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 10.725471 KDa
SequenceString:
MEMLPLVKIA PEYNLTLDPS TGMIGAALGR EVIILSMDEI NEQIAALEAT ADDLINSLDP TTIPEGSYPG REGVYLTAGK LTNIVYGFI LGLIILFALL L

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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 27.132244 KDa
SequenceString: MSVAAGGPAG AAIPESRLMA LGILGGLAGI YASAVNPVIG PVLASLGAVC AIVWGADAIR RVASYGLGTG VPSIGYMSVS IGIVGVVAG LASVFVVPAI AVPVVALILA MILGVVVAVL GKKIVKMKIP ILEKCTAEIS GAAALSVLGF SAAIAGSYTL Q TMLTSVIT ...String:
MSVAAGGPAG AAIPESRLMA LGILGGLAGI YASAVNPVIG PVLASLGAVC AIVWGADAIR RVASYGLGTG VPSIGYMSVS IGIVGVVAG LASVFVVPAI AVPVVALILA MILGVVVAVL GKKIVKMKIP ILEKCTAEIS GAAALSVLGF SAAIAGSYTL Q TMLTSVIT TGFIGLLFIL NTMAIQHPFN ACLGPNENQT RTLKLAASTG FISMAIVGLL GIGLNPSWWL VSLIGALCWI VA FRAFVSA SFEEAASVKW SGLWPKEEEH

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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 22.783881 KDa
SequenceString: MDPLLLIGAI TAGGVLIGGG VHFVPVGGAP AAMATATGVG TGTAMLAAGA GLTGLITAAA MTGQSPLMIM AAGAVGSMLM IGITMLVGN LIYVFGVGTV PVSAKVSVDP ITGMEQEKYV TPGTEGHGLP TVCFVSGIIG GALGGIGGGL IYWALNEALK T LSYGAMGA ...String:
MDPLLLIGAI TAGGVLIGGG VHFVPVGGAP AAMATATGVG TGTAMLAAGA GLTGLITAAA MTGQSPLMIM AAGAVGSMLM IGITMLVGN LIYVFGVGTV PVSAKVSVDP ITGMEQEKYV TPGTEGHGLP TVCFVSGIIG GALGGIGGGL IYWALNEALK T LSYGAMGA AGVAAIFAVG IFFINAVIAS YNIGGTIEGF HDPKFKRIGR GIVACLIASI VAGALSTLLV YGGVF

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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 31.253289 KDa
SequenceString: MDPMITGLGV VALMGAAATI AGAAEDLESD VGSQSNPNSQ VQLAPQMGHL HRIINKAVSG EPVAYGTWCG IAGSVAFVLM NSMQLPVIM AIAIGAVIAA MVHTTYAVTS HMGRIVSQSQ FNQPLFMDML VQHLGPIAGH GFIVTFCTVG LSYLMTLPIP G FAHPFPLP ...String:
MDPMITGLGV VALMGAAATI AGAAEDLESD VGSQSNPNSQ VQLAPQMGHL HRIINKAVSG EPVAYGTWCG IAGSVAFVLM NSMQLPVIM AIAIGAVIAA MVHTTYAVTS HMGRIVSQSQ FNQPLFMDML VQHLGPIAGH GFIVTFCTVG LSYLMTLPIP G FAHPFPLP LLAVLWGITI GAIGSSTGDV HYGAEREYQQ YPFGGGIPVA IHGDITTKAE LGARNSMDVV HFCAKYGGPL TG FAFGAIV FLSFWNTIVF GITGGIISGL IIVLLLIILN NRLEVFARNR YGPYKEEE

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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 7.325928 KDa
SequenceString:
MIILSNKPNI RGIKNVVEDI KYRNQLIGRD GRLFAGLIAT RISGIAIGFL LAVLLVGVPA MMSILGVI

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
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 9.519042 KDa
SequenceString:
MSEEEKTTIP RVLVSADEFN KANEKLDEIE EKVEFTVGEY SQRIGQQIGR DIGILYGIVI GLIILAVTNI LFAGLLKGLL KSLFGL

UniProtKB: Tetrahydromethanopterin S-methyltransferase subunit G

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39...

MacromoleculeName: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5- ...Name: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate
type: ligand / ID: 9 / Number of copies: 12 / Formula: JCV
Molecular weightTheoretical: 1.706543 KDa

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Macromolecule #10: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 10 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 208 / 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 73.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138464
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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