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

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Basic information

Entry
Database: PDB / ID: 9qtr
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Components
  • Conserved protein
  • Tetrahydromethanopterin S-methyltransferase subunit A
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 / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / Tetrahydromethanopterin S-methyltransferase subunit A / Conserved protein
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / 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

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Assembly

Deposited unit
A: Tetrahydromethanopterin S-methyltransferase subunit A
i: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3403
Polymers33,0192
Non-polymers1,3211
Water00
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

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


Mass: 25395.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina mazei Go1 (archaea)
References: UniProt: O59640, tetrahydromethanopterin S-methyltransferase
#2: Protein Conserved protein


Mass: 7623.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina mazei Go1 (archaea) / References: UniProt: Q8PUD4
#3: 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
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-#2 / 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 softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136531 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.8 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00261731
ELECTRON MICROSCOPYf_angle_d0.65352377
ELECTRON MICROSCOPYf_chiral_restr0.048275
ELECTRON MICROSCOPYf_plane_restr0.0066302
ELECTRON MICROSCOPYf_dihedral_angle_d14.4695301

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