Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound

Experimental Data Snapshot

  • Resolution: 3.13 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The structural basis of RNA-catalyzed RNA polymerization.

Shechner, D.M.Bartel, D.P.

(2011) Nat Struct Mol Biol 18: 1036-1042

  • DOI: https://doi.org/10.1038/nsmb.2107
  • Primary Citation of Related Structures:  
    3R1H, 3R1L

  • PubMed Abstract: 

    Early life presumably required polymerase ribozymes capable of replicating RNA. Known polymerase ribozymes best approximating such replicases use as their catalytic engine an RNA-ligase ribozyme originally selected from random RNA sequences. Here we report 3.15-Å crystal structures of this ligase trapped in catalytically viable preligation states, with the 3'-hydroxyl nucleophile positioned for in-line attack on the 5'-triphosphate. Guided by metal- and solvent-mediated interactions, the 5'-triphosphate hooks into the major groove of the adjoining RNA duplex in an unanticipated conformation. Two phosphates and the nucleophile jointly coordinate an active-site metal ion. Atomic mutagenesis experiments demonstrate that active-site nucleobase and hydroxyl groups also participate directly in catalysis, collectively playing a role that in proteinaceous polymerases is performed by a second metal ion. Thus artificial ribozymes can use complex catalytic strategies that differ markedly from those of analogous biological enzymes.

  • Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A
A, D
98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
GTEx:  ENSG00000077312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
B, E
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Class I ligase ribozyme
C, F
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth F],
G [auth C],
GA [auth F],
H [auth C],
HA [auth F],
I [auth C],
IA [auth F],
J [auth C],
JA [auth F],
K [auth C],
KA [auth F],
L [auth C],
LA [auth F],
M [auth C],
MA [auth F],
N [auth C],
NA [auth F],
O [auth C],
OA [auth F],
P [auth C],
PA [auth F],
Q [auth C],
QA [auth F],
R [auth C],
RA [auth F],
S [auth C],
SA [auth F],
T [auth C],
TA [auth F],
U [auth C],
UA [auth F],
V [auth C],
VA [auth F],
W [auth C],
WA [auth F],
X [auth C],
XA [auth F],
Y [auth C],
YA [auth F],
Z [auth C],
ZA [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.13 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.19α = 99.86
b = 70.237β = 99.34
c = 71.214γ = 103.81
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description