6C8M

RNA-activated 2-AIpG monomer, 1.5h soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic observation of nonenzymatic RNA primer extension.

Zhang, W.Walton, T.Li, L.Szostak, J.W.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.36422
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of lif ...

    The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.


    Organizational Affiliation

    Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')A15synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')B14synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQ1
Query on EQ1

Download SDF File 
Download CCD File 
A
[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic acid
C23 H30 N13 O14 P2
VUFFAXSZAZXUSC-XPWFQUROSA-N
 Ligand Interaction
EQ4
Query on EQ4

Download SDF File 
Download CCD File 
A
5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine
C13 H17 N8 O7 P
UJFHHYLHXPKINK-IOSLPCCCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LCG
Query on LCG
A, B
RNA LINKINGC11 H14 N5 O8 PDG
LCC
Query on LCC
A, B
RNA LINKINGC11 H16 N3 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.874α = 90.00
b = 47.874β = 90.00
c = 82.731γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references