7JJD

Sarcin-ricin loop with guanosine monothiophosphate residue.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.173 

wwPDB Validation   3D Report Full Report



Literature

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.

Pallan, P.S., Lybrand, T.P., Schlegel, M.K., Harp, J.M., Jahns, H., Manoharan, M., Egli, M.

(2020) Biochemistry 59: 4627-4637

  • DOI: 10.1021/acs.biochem.0c00685
  • Primary Citation of Related Structures:  
    7JJE, 7JJF, 7JJD

  • PubMed Abstract: 

    • GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by G ApGA, and the phosphate p stacks on G . We r ...

    GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by G ApGA, and the phosphate p stacks on G . We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2···G and R p-PSO···G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 °C in melting temperature T m and -4.7 kcal/mol in ΔΔ G °. Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 Å longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 Å for S vs 1.52 Å for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.

    Organizational Affiliation: 

    Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (27-MER)A27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.173 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.639α = 90
b = 29.639β = 90
c = 76.658γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History 

  • Version 1.0: 2020-12-23
    Type: Initial release