6C8E

RNA-imidazolium-bridged intermediate complex, 4h soaking

  • Classification: RNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2018-01-24 Released: 2018-05-30 
  • Deposition Author(s): Zhang, W., Szostak, J.W.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 

Starting Model: experimental
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This is version 2.0 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: https://doi.org/10.7554/eLife.36422
  • Primary Citation of Related Structures:  
    6C8D, 6C8E, 6C8I, 6C8J, 6C8K, 6C8L, 6C8M, 6C8N, 6C8O, 6CAB

  • 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 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

    Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
A, B
14synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EQ1
Query on EQ1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-amino-1-[(R)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium
C23 H30 N13 O14 P2
NQKWYRRUFGLPHK-XPWFQUROSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.023α = 90
b = 49.023β = 90
c = 81.317γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-05-01
    Changes: Derived calculations, Non-polymer description, Structure summary