Extended Data Table 2:

Cryo-EM Data Collection, Refinement, and Validation Statistics.

	METTL1-WDR4-tRNA (EMDB-27264) (PDB 8D9K)	METTL1-WDR4-tRNA-SAM (EMDB-27265) (PDB 8D9L)	METTL1-WDR4-tRNA-SAH (EMDB-28108) (PDB 8EG0)
Data collection and processing
Microscope	Titan Krios	Titan Krios	Titan Krios
Magnification	105,000x	105,000x	105,000x
Voltage (kV)	300	300	300
Electron exposure (e–/Å2)	62	62	62
Exposure time (s)	5.5	5.5	5.5
Defocus range (μm)	0.7 – 2.2	0.7 – 2.2	0.7 – 2.2
Pixel size (Å)	0.415	0.415	0.415
Number of frames	62	62	62
Energy filter slit width (keV)	20	20	20
Symmetry imposed	CI	CI	CI
Number of micrographs	16,993	5,607	6,120
Initial particle images (no.)	2,531,779	395,556	899,325
Particles used for 3DVA (no.)	1,571,798	321,258	594,087
Final particle images (no.)	37,033	34,558	71,913
Map resolution (Å)	3.72 / 4.20	4.05/4.70	3.53/4.10
0.143 FSC (masked/unmasked)
Map resolution range (Å)	2.5-4	3-5	2.5-4
Refinement
Software	Phenix	Phenix	Phenix
Initial model used (PDB code)	8D58 – 7MRL	8D58 – 7MRL	8D58 – 7MRL
Model resolution (Å)	3.7 (0.143)	4.1 (0.143)	3.5 (0.143)
FSC threshold
Model resolution range (Å)	2.5-4	3-5	2.5-4
Map sharpening B factor (Å2)	−138	−168	−149
Model composition
Non-hydrogen atoms	5708	5757	6031
Protein residues	546	553	584
Nucleotide residues	65	65	65
Ligands	None	SAM	SAH
B factors (Å2)
Protein	160.96	245.13	182.88
Nucleotide	255.72	338.24	248.42
Ligand		255.74	182.8
R.m.s. deviations
Bond lengths (Å)	0.001	0.001	0.002
Bond angles (°)	0.364	0.385	0.420
Validation
MolProbity score	1.35	1.40	1.43
Clashscore	6.27	7.25	7.87
Poor rotamers (%)	0.64	0.43	0.00
Ramachandran plot
Favored (%)	98.13	98.15	99.47
Allowed (%)	1.87	1.85	0.53
Disallowed (%)	0.00	0.00	0.00