5JS2

Human Argonaute-2 Bound to a Modified siRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.954 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.

Schirle, N.T.Kinberger, G.A.Murray, H.F.Lima, W.F.Prakash, T.P.MacRae, I.J.

(2016) J.Am.Chem.Soc. 138: 8694-8697

  • DOI: 10.1021/jacs.6b04454
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Incorporation of chemical modifications into small interfering RNAs (siRNAs) increases their metabolic stability and improves their tissue distribution. However, how these modifications impact interactions with Argonaute-2 (Ago2), the molecular targe ...

    Incorporation of chemical modifications into small interfering RNAs (siRNAs) increases their metabolic stability and improves their tissue distribution. However, how these modifications impact interactions with Argonaute-2 (Ago2), the molecular target of siRNAs, is not known. Herein we present the crystal structure of human Ago2 bound to a metabolically stable siRNA containing extensive backbone modifications. Comparison to the structure of an equivalent unmodified-siRNA complex indicates that the structure of Ago2 is relatively unaffected by chemical modifications in the bound siRNA. In contrast, the modified siRNA appears to be much more plastic and shifts, relative to the unmodified siRNA, to optimize contacts with Ago2. Structure-activity analysis reveals that even major conformational perturbations in the 3' half of the siRNA seed region have a relatively modest effect on knockdown potency. These findings provide an explanation for a variety of modification patterns tolerated in siRNAs and a structural basis for advancing therapeutic siRNA design.


    Organizational Affiliation

    Department of Integrative Computational and Structural Biology, The Scripps Research Institute , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-2
A
859Homo sapiensMutation(s): 1 
Gene Names: AGO2 (EIF2C2)
EC: 3.1.26.n2
Find proteins for Q9UKV8 (Homo sapiens)
Go to Gene View: AGO2
Go to UniProtKB:  Q9UKV8
Entity ID: 2
MoleculeChainsLengthOrganism
modified siRNAB6synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IPH
Query on IPH

Download SDF File 
Download CCD File 
A
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
6OO
Query on 6OO
B
RNA linkingC10 H16 N3 O7 P SC
6NW
Query on 6NW
B
RNA linkingC11 H16 N5 O6 P SA
UFT
Query on UFT
B
DNA LINKINGC9 H12 F N2 O8 PDU
6OP
Query on 6OP
B
RNA linkingC14 H21 N2 O9 P

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F2T
Query on F2T
B
RNA linkingC9 H12 F N2 O7 P SU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.954 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.102α = 90.00
b = 107.552β = 107.39
c = 68.893γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references