5V2H

RNA octamer containing glycol nucleic acid, SgnT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08001 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.

Schlegel, M.K.Foster, D.J.Kel'in, A.V.Zlatev, I.Bisbe, A.Jayaraman, M.Lackey, J.G.Rajeev, K.G.Charisse, K.Harp, J.Pallan, P.S.Maier, M.A.Egli, M.Manoharan, M.

(2017) J. Am. Chem. Soc. 139: 8537-8546

  • DOI: 10.1021/jacs.7b02694
  • Primary Citation of Related Structures:  5V1K, 5V1L

  • PubMed Abstract: 
  • Here we report the investigation of glycol nucleic acid (GNA), an acyclic nucleic acid analogue, as a modification of siRNA duplexes. We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three ind ...

    Here we report the investigation of glycol nucleic acid (GNA), an acyclic nucleic acid analogue, as a modification of siRNA duplexes. We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three individual crystal structures. These structures indicate that the (S)-nucleotide backbone adopts a conformation that has little impact on the overall duplex structure, while the (R)-nucleotide disrupts the phosphate backbone and hydrogen bonding of an adjacent base pair. In addition, the GNA-T nucleobase adopts a rotated conformation in which the 5-methyl group points into the minor groove, rather than the major groove as in a normal Watson-Crick base pair. This observation of reverse Watson-Crick base pairing is further supported by thermal melting analysis of GNA-C and GNA-G containing duplexes where it was demonstrated that a higher thermal stability was associated with isoguanine and isocytosine base pairing, respectively, over the canonical nucleobases. Furthermore, it was also shown that GNA nucleotide or dinucleotide incorporation increases resistance against snake venom phosphodiesterase. Consistent with the structural data, modification of an siRNA with (S)-GNA resulted in greater in vitro potencies over identical sequences containing (R)-GNA. A walk of (S)-GNA along the guide and passenger strands of a GalNAc conjugate duplex targeting mouse transthyretin (TTR) indicated that GNA is well tolerated in the seed region of both strands in vitro, resulting in an approximate 2-fold improvement in potency. Finally, these conjugate duplexes modified with GNA were capable of maintaining in vivo potency when subcutaneously injected into mice.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')A,B,C,D8synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ZTH
Query on ZTH
A, B, C, D
RNA LINKINGC8 H13 N2 O7 PT
CBV
Query on CBV
A, B, C, D
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08001 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.136 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.029α = 90.00
b = 31.901β = 90.46
c = 33.782γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXDphasing
PHENIXrefinement
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-04 
  • Released Date: 2017-06-14 
  • Deposition Author(s): Harp, J.M., Egli, M.

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-12
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description