Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI.
Journal, issue, pages	Nat Commun, Year 2025
Publish date	Dec 23, 2025
Authors	Tristan Reif-Trauttmansdorff / Eva Herdering / Stefan Bohn / Tomas Pascoa / Jörg Kahnt / Erik Zimmer / Anuj Kumar / Ruth A Schmitz / Jan M Schuller /
PubMed Abstract	Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase ...Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase complex: the N⁵-tetrahydromethanopterin:CoM-S-methyltransferase (Mtr). It couples methyl transfer between two methanogen-specific cofactors with sodium ion transport across the membrane, forming the only energy-conserving step in hydrogenotrophic methanogenesis. Here, we present a 2.1 Å single-particle cryo-EM structure of the Mtr complex from Methanosarcina mazei. The structure reveals the organization of all catalytic subunits, embedded archaeal lipids and the sodium-binding site. Most strikingly, we discover MtrI, a previously unannotated small open-reading frame encoded protein ( < 100 aa) found within the order of Methanosarcinales that binds both the top of the sodium-channel and cytosolic domain of MtrA via its cobamide cofactor in response to oxygen exposure. This interaction likely prevents sodium leakage and stabilizes the complex under oxidative conditions, revealing an unexpected regulatory mechanism in methanogen energy conservation.
External links	Nat Commun / PubMed:41436738
Methods	EM (single particle)
Resolution	2.1 - 3.2 Å
Structure data	53358 9qtp EMDB-53358, PDB-9qtp: Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder Method: EM (single particle) / Resolution: 3.2 Å 53359 9qtq EMDB-53359, PDB-9qtq: Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder Method: EM (single particle) / Resolution: 2.1 Å 53360 9qtr EMDB-53360, PDB-9qtr: Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder Method: EM (single particle) / Resolution: 2.5 Å 53361 9qts EMDB-53361, PDB-9qts: Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder Method: EM (single particle) / Resolution: 2.1 Å
Chemicals	PDB-1jap: COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) ChemComp-L1P: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL PDB-1jao: COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) ChemComp-NA: Unknown entry PDB-1jan: COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (PHE79 FORM) ChemComp-HOH: WATER ChemComp-B13: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
Source	methanosarcina mazei go1 (archaea)
Keywords	MEMBRANE 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