› 5cd1

X-ray diffraction
3.6Å resolution

Structure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex with SAH and tRNA3Lys

Released:
DOI: 10.2210/pdb5cd1/pdb
PDB entry 5cd1 coloured by chain, front view.
PDB entry 5cd1 coloured by chain, side view.
PDB entry 5cd1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA(3)(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.
Finer-Moore J, Czudnochowski N, O'Connell JD, Wang AL, Stroud RM
J Mol Biol 427 3862-76 (2015)
PMID: 26470919

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine(58) in tRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(58) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188508 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A Chains: A, D
Molecule details ›
Chains: A, D
Length: 289 amino acids
Theoretical weight: 31.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96FX7 (Residues: 1-289; Coverage: 100%)
Gene names: C14orf172, TRM61, TRMT61A
Sequence domains: tRNA methyltransferase complex GCD14 subunit
Structure domains:
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 Chains: B, E
Molecule details ›
Chains: B, E
Length: 497 amino acids
Theoretical weight: 55.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UJA5 (Residues: 1-497; Coverage: 100%)
Gene names: CGI-09, KIAA1153, TRM6, TRMT6
Sequence domains: Gcd10p family
tRNA3Lys Chains: M, N
Molecule details ›
Chains: M, N
Length: 77 nucleotides
Theoretical weight: 24.79 KDa
Sequence domains: tRNA

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 128.24Å b: 137.44Å c: 157.59Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.232 0.273
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

RNA-modifying proteins as anticancer drug targets.
Boriack-Sjodin et al. (2018)
3 more

3 mentions without citation

The diverse structural modes of tRNA binding and recognition.
Biela et al. (2023)
2 more