› 7p8q

X-ray diffraction
2.29Å resolution

Structure of E.coli RlmJ in complex with an RNA conjugate (GA-SAM)

Released:
DOI: 10.2210/pdb7p8q/pdb
PDB entry 7p8q coloured by chain, front view.
PDB entry 7p8q coloured by chain, side view.
PDB entry 7p8q coloured by chain, top view.
Source organisms:
Primary publication:
Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Meynier V, Iannazzo L, Catala M, Oerum S, Braud E, Atdjian C, Barraud P, Fonvielle M, Tisné C, Ethève-Quelquejeu M
OpenAccess logo Nucleic Acids Res 50 5793-5806 (2022)
PMID: 35580049

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + N(6)-methyladenine(2030) in 23S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153452 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Ribosomal RNA large subunit methyltransferase J Chain: A
Molecule details ›
Chain: A
Length: 280 amino acids
Theoretical weight: 31.99 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37634 (Residues: 1-280; Coverage: 100%)
Gene names: JW3466, b3499, rlmJ, yhiR
Sequence domains: Ribosomal RNA large subunit methyltransferase D, RlmJ
RNA conjugate (GA-SAM) Chain: B
Molecule details ›
Chain: B
Length: 2 nucleotides
Theoretical weight: 549 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand 6D6 1 x 6D6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: C2
Unit cell:
a: 80.32Å b: 38.3Å c: 90.8Å
α: 90° β: 105.36° γ: 90°
R-values:
R R work R free
0.221 0.218 0.275
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 mention without citation

Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Meynier et al. (2022)