3IVK: Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment

Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.
PDB ID: 3IVKDownload
MMDB ID: 80458
PDB Deposition Date: 2009/9/1
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 3IVK: trimeric; determined by author and by software (PISA)
Molecular Components in 3IVK
Label Count Molecule
Proteins (2 molecules)
FAB Light Chain
Molecule annotation
FAB Heavy Chain
Molecule annotation
Nucleotide(1 molecule)
Class I Ligase Product
Molecule annotation
Chemicals (15 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB