5VAJ

BhRNase H - amide-RNA/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.

Mutisya, D.Hardcastle, T.Cheruiyot, S.K.Pallan, P.S.Kennedy, S.D.Egli, M.Kelley, M.L.Smith, A.V.B.Rozners, E.

(2017) Nucleic Acids Res. 45: 8142-8155

  • DOI: 10.1093/nar/gkx558

  • PubMed Abstract: 
  • While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as ...

    While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA-DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.


    Organizational Affiliation

    Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A, B
142Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Gene Names: rnhA
EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KEI9
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3')C11synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')D12synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
URU
Query on URU
C
RNA LINKINGC20 H26 N5 O14 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 137.180α = 90.00
b = 37.513β = 121.65
c = 93.863γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-27 
  • Released Date: 2017-09-13 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM71461

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release