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- PDB-9qts: Structure of the energy converting methyltransferase (Mtr) of Met... -

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Basic information

Entry
Database: PDB / ID: 9qts
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Components
  • (Tetrahydromethanopterin S-methyltransferase subunit ...) x 8
  • Conserved protein
KeywordsMEMBRANE PROTEIN / Sodium-pumping / membrane-bound / methyltransferase complex / methanogen / methanogenic / methylotrophic / archaeon / archaea / methanosarcina / methanosarcina mazei / Vitamin B12 / corrinoid / cobalt / 5-hydroxybenzimidazole / small protein / oxygen-sensitive
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
: / : / : / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 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 ...: / : / : / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsReif-Trauttmansdorff, T. / Herdering, E. / Bohn, S. / Pascoa, T.C. / Kumar, A. / Zimmer, E. / Schmitz, R.A. / Schuller, J.M.
Funding supportEuropean Union, 1items
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, T.C. / Kumar, A. / Zimmer, E. / Schmitz, R.A. / Schuller, J.M.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrahydromethanopterin S-methyltransferase subunit A
B: Tetrahydromethanopterin S-methyltransferase subunit A
C: Tetrahydromethanopterin S-methyltransferase subunit A
D: Tetrahydromethanopterin S-methyltransferase subunit B
E: Tetrahydromethanopterin S-methyltransferase subunit B
F: Tetrahydromethanopterin S-methyltransferase subunit B
G: Tetrahydromethanopterin S-methyltransferase subunit C
H: Tetrahydromethanopterin S-methyltransferase subunit C
I: Tetrahydromethanopterin S-methyltransferase subunit C
J: Tetrahydromethanopterin S-methyltransferase subunit D
K: Tetrahydromethanopterin S-methyltransferase subunit D
L: Tetrahydromethanopterin S-methyltransferase subunit D
M: Tetrahydromethanopterin S-methyltransferase subunit E
N: Tetrahydromethanopterin S-methyltransferase subunit E
O: Tetrahydromethanopterin S-methyltransferase subunit E
P: Tetrahydromethanopterin S-methyltransferase subunit F
Q: Tetrahydromethanopterin S-methyltransferase subunit F
R: Tetrahydromethanopterin S-methyltransferase subunit F
S: Tetrahydromethanopterin S-methyltransferase subunit G
T: Tetrahydromethanopterin S-methyltransferase subunit G
U: Tetrahydromethanopterin S-methyltransferase subunit G
i: Conserved protein
m: Tetrahydromethanopterin S-methyltransferase subunit H
n: Tetrahydromethanopterin S-methyltransferase subunit H
o: Tetrahydromethanopterin S-methyltransferase subunit H
p: Tetrahydromethanopterin S-methyltransferase subunit H
q: Tetrahydromethanopterin S-methyltransferase subunit H
r: Tetrahydromethanopterin S-methyltransferase subunit H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,70547
Polymers634,03528
Non-polymers13,66919
Water47,5782641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Tetrahydromethanopterin S-methyltransferase subunit ... , 8 types, 27 molecules ABCDEFGHIJKLMNOPQRSTUmnopqr

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 25395.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrA, MM_1543 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: O59640, tetrahydromethanopterin S-methyltransferase
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit B / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit B


Mass: 11879.630 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrB, MM_1544 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80655, tetrahydromethanopterin S-methyltransferase
#3: Protein Tetrahydromethanopterin S-methyltransferase subunit C / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit C


Mass: 26953.893 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrC, MM_1545 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: O59638, tetrahydromethanopterin S-methyltransferase
#4: Protein Tetrahydromethanopterin S-methyltransferase subunit D / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit D


Mass: 25279.777 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrD, MM_1546 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80653, tetrahydromethanopterin S-methyltransferase
#5: Protein Tetrahydromethanopterin S-methyltransferase subunit E / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit E


Mass: 35539.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: c-terminal Twin-StrepTag / Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrE, MM_1547 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80651, tetrahydromethanopterin S-methyltransferase
#6: Protein Tetrahydromethanopterin S-methyltransferase subunit F / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit F


Mass: 7573.959 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrF, MM_1542 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80654, tetrahydromethanopterin S-methyltransferase
#7: Protein Tetrahydromethanopterin S-methyltransferase subunit G / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit G


Mass: 8030.405 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrG, MM_1541 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80656, tetrahydromethanopterin S-methyltransferase
#9: Protein
Tetrahydromethanopterin S-methyltransferase subunit H / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit H


Mass: 34075.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrH, MM_1540 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80650, tetrahydromethanopterin S-methyltransferase

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Protein , 1 types, 1 molecules i

#8: Protein Conserved protein


Mass: 7623.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: MM_2401 / Production host: Methanosarcina mazei Go1 (archaea) / References: UniProt: Q8PUD4

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Non-polymers , 7 types, 2660 molecules

#10: Chemical ChemComp-B13 / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE


Mass: 1321.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60H88CoN13O15P / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-A1JAP / 2-Hydroxy-archaetidylinositol / (2~{S})-2-azanyl-3-[oxidanyl-[(2~{S})-3-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]-2-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethyl-3-oxidanyl-hexadecoxy]propoxy]phosphoryl]oxy-propanoic acid


Mass: 836.214 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H94NO9P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-L1P / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE


Mass: 733.137 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C43H89O6P / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-A1JAO / Archaetidylinositol / [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] [(2~{S})-3-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]-2-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethyl-3-oxidanyl-hexadecoxy]propyl] hydrogen phosphate


Mass: 911.277 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H99O12P / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-A1JAN / Archaetidylethanolamine / 2-azanylethyl [(2~{S})-2,3-bis[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]propyl] hydrogen phosphate


Mass: 776.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H94NO6P / Feature type: SUBJECT OF INVESTIGATION
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2641 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mtr complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Buffer solutionpH: 7
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002242176
ELECTRON MICROSCOPYf_angle_d0.431457260
ELECTRON MICROSCOPYf_chiral_restr0.03866797
ELECTRON MICROSCOPYf_plane_restr0.00377144
ELECTRON MICROSCOPYf_dihedral_angle_d8.6336419

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