3IVK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the catalytic core of an RNA-polymerase ribozyme.

Shechner, D.M.Grant, R.A.Bagby, S.C.Koldobskaya, Y.Piccirilli, J.A.Bartel, D.P.

(2009) Science 326: 1271-1275

  • DOI: https://doi.org/10.1126/science.1174676
  • Primary Citation of Related Structures:  
    3HHN, 3IVK

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainA [auth L],
C [auth B]
213Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainB [auth H],
D [auth A]
224Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
class I ligase productE [auth M],
F [auth C]
128N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

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G [auth L],
J [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL
Query on CL

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I [auth L],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AA [auth M]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth M],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
H [auth L],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
L [auth M],
LA [auth C],
M,
MA [auth C],
N [auth M],
NA [auth C],
O [auth M],
OA [auth C],
P [auth M],
PA [auth C],
Q [auth M],
QA [auth C],
R [auth M],
S [auth M],
T [auth M],
U [auth M],
V [auth M],
W [auth M],
X [auth M],
Y [auth M],
Z [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.499α = 90
b = 206.452β = 90
c = 135.926γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description