SMTL ID : 4qtu.1 (1 other biounit)

Structure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S rRNA (SAM bound form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.11, V.13, C.16, C.112, C.115 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.16, A:C.112, A:C.115

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: K.14, L.134 Chain B: N.131, R.139 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: L.34, Q.36 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: H.117, I.118, Y.119, Y.120, N.127, L.129 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: L.48, D.52, F.78, P.79, S.80 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: T.86, D.87 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: I.92 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain B: Y.159 Ligands: SAM.8 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.14 Chain B: M.138, R.139, N.142, T.143 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: L.170, K.174, F.178, S.179, G.180, L.199 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain B: E.188 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: S.25, T.26, R.27 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: Q.67, E.68 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: N.43 Chain B: D.70, H.71, V.72, E.92 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: L.40, L.45, Q.46, P.47, E.68, G.69, H.71 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: I.12, Y.14, S.79, P.80, S.81 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: R.38, L.42 Ligand excluded by PLIP

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.8: 21 residues within 4Å: Chain B: Y.14, Y.22, Q.32, G.55, C.56, G.57, L.60, S.61, D.77, I.78, S.79, M.82, Q.98, D.99, M.100, I.117, S.118, A.119, W.122, R.136 Ligands: EDO.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.32, B:G.55, B:S.61, B:I.78, B:S.79, B:D.99, B:M.100, B:I.117, B:R.136 Water bridges: B:L.60, B:I.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Letoquart, J. et al., Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-12-24

Peptides

Multifunctional methyltransferase subunit TRM112: A
Putative methyltransferase BUD23: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Multifunctional methyltransferase subunit TRM112

Putative methyltransferase BUD23

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