SMTL ID : 8p7c.1

CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain C: W.45, Y.49, R.60, G.87, G.89, G.91, N.92, C.93, D.110, F.111, C.135, D.136, L.137, T.138, I.157, F.158, V.159, A.162, V.163 Chain D: C.32 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.49, C:Y.49, C:G.87, C:F.111, C:D.136, C:L.137, C:I.157 Salt bridges: C:R.60 pi-Stacking: C:F.111, C:F.111 SAH.5: 20 residues within 4Å: Chain E: W.45, Y.49, R.60, G.87, G.89, G.91, N.92, C.93, D.110, F.111, C.135, D.136, L.137, T.138, I.157, F.158, V.159, A.162, V.163 Chain F: C.32 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.49, E:Y.49, E:G.87, E:F.111, E:D.136, E:L.137, E:I.157 Salt bridges: E:R.60 pi-Stacking: E:F.111, E:F.111

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain D: G.9, C.11, N.12 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain D: C.57, U.59 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain F: G.9, C.11, N.12 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain F: C.57, U.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Throll, P. et al., Structural basis of tRNA recognition by the m 3 C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-06-12

Peptides

Serine--tRNA ligase, cytoplasmic: AB
tRNA N(3)-methylcytidine methyltransferase METTL6: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

E
C

Serine--tRNA ligase, cytoplasmic

tRNA N(3)-methylcytidine methyltransferase METTL6

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