› 7p3b

X-ray diffraction
2.3Å resolution

Human RNA ligase RTCB in complex with GMP and Co(II)

Released:
DOI: 10.2210/pdb7p3b/pdb
PDB entry 7p3b coloured by chain, front view.
PDB entry 7p3b coloured by chain, side view.
PDB entry 7p3b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular architecture of the human tRNA ligase complex.
Kroupova A, Ackle F, Asanović I, Weitzer S, Boneberg FM, Faini M, Leitner A, Chui A, Aebersold R, Martinez J, Jinek M
Elife 10 (2021)
PMID: 34854379

Function and Biology Details

Reaction catalysed: 
(1a) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-N(tau)-phosphono-L-histidine + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195208 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-splicing ligase RtcB homolog Chains: A, B
Molecule details ›
Chains: A, B
Length: 507 amino acids
Theoretical weight: 55.43 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y3I0 (Residues: 2-505; Coverage: 100%)
Gene names: C22orf28, HSPC117, RTCB
Sequence domains: tRNA-splicing ligase RtcB

Ligands and Environments

5 bound ligands:
Ligand 5GP 2 x 5GP
Ligand CO 4 x CO
Ligand ACT 2 x ACT
Ligand FMT 4 x FMT
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P41212
Unit cell:
a: 96.906Å b: 96.906Å c: 227.137Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.22
Expression system: Spodoptera frugiperda

Quick links

Citations

4 review citations

Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex.
Hayne et al. (2022)
3 more

2 mentions without citation

Molecular architecture of the human tRNA ligase complex.
Kroupova et al. (2021)
1 more