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	Mechanism for the substrate recognition by a eukaryotic DNA N-adenine methyltransferase complex.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 8690, Year 2025
Publish date	Sep 30, 2025
Authors	Qi Xu / Ying Xie / Zhubing Shi /
PubMed Abstract	In eukaryotes, DNA N-methyladenine (6mA) modification plays important roles in various cellular functions, such as chromatin dynamics, gene expression regulation, and DNA damage response. It remains ...In eukaryotes, DNA N-methyladenine (6mA) modification plays important roles in various cellular functions, such as chromatin dynamics, gene expression regulation, and DNA damage response. It remains largely unknown how eukaryotic DNA 6mA methyltransferases (MTases) recognize their substrates. Here, we reported the structures of DNA-bound eukaryotic 6mA MTase complexes. The MTA1 complex (MTA1c) in ciliates is composed of MTA1, MTA9 (or MTA9-B), p1 and p2 subunits. Cryo-electron microscopy structures of MTA1c-DNA complexes reveal that DNA lies on the surface of the MTA1-MTA9/9-B dimer and is clamped by the p1 N-terminal region. The target deoxyadenosine is flipped out of the DNA duplex and approaches the catalytic center. Unmethylated and hemi-methylated DNA substrates bind MTA1c with differential conformational dynamics. Our structural and biochemical studies shed light on the activation and substrate recognition of MTA1c and provide a framework for understanding the molecular mechanism of DNA 6mA modification in eukaryotes.
External links	Nat Commun / PubMed:41027852 / PubMed Central
Methods	EM (single particle)
Resolution	2.54 - 3.29 Å
Structure data	38777 8xyl EMDB-38777, PDB-8xyl: Cryo-EM structure of Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 2.79 Å 38780 8xyp EMDB-38780, PDB-8xyp: Cryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 2.54 Å 38781 8xyq EMDB-38781, PDB-8xyq: Cryo-EM structure of SAM-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 2.8 Å 38782 8xyx EMDB-38782, PDB-8xyx: Cryo-EM structure of SAM-bound Tetrahymena DNA methyltransferase complex MTA1c (D209A) Method: EM (single particle) / Resolution: 2.8 Å EMDB-38786: Cryo-EM structure of DNA-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 3.27 Å EMDB-38787: Cryo-EM structure of DNA-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 3.28 Å 63956 9u92 EMDB-63956, PDB-9u92: Cryo-EM structure of Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 2.68 Å 63961 9u9e EMDB-63961, PDB-9u9e: Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 2.89 Å 63963 9vu6 EMDB-63963: Cryo-EM structure of DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B) PDB-9vu6: Cryo-EM structure of unmethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B) Method: EM (single particle) / Resolution: 3.29 Å 63967 9u9k EMDB-63967, PDB-9u9k: Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B) Method: EM (single particle) / Resolution: 2.96 Å EMDB-63970: Cryo-EM structure of DNA-bound Tetrahymena DNA methyltransferase complex MTA1c Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE ChemComp-SAM: S-ADENOSYLMETHIONINE
Source	tetrahymena thermophila sb210 (eukaryote) synthetic construct (others)
Keywords	DNA BINDING PROTEIN / DNA methyltransferase / DNA N6-methyladenine modification / chromatin regulation / gene regulation / protein-DNA complex / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex