5VM9

Human Argonaute3 bound to guide RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Human Argonaute3 has slicer activity.

Park, M.S.Phan, H.D.Busch, F.Hinckley, S.H.Brackbill, J.A.Wysocki, V.H.Nakanishi, K.

(2017) Nucleic Acids Res. 45: 11867-11877

  • DOI: 10.1093/nar/gkx916

  • PubMed Abstract: 
  • Of the four human Argonaute (AGO) paralogs, only AGO2 has been shown to have slicer activity. The others (AGO1, AGO3 and AGO4) have been thought to assemble with microRNAs to form slicer-independent effector complexes that bind target mRNAs and silen ...

    Of the four human Argonaute (AGO) paralogs, only AGO2 has been shown to have slicer activity. The others (AGO1, AGO3 and AGO4) have been thought to assemble with microRNAs to form slicer-independent effector complexes that bind target mRNAs and silence gene expression through translational repression and deadenylation but not cleavage. Here, we report that recombinant AGO3 loaded with miR-20a cleaves complementary target RNAs, whereas AGO3 loaded with let-7a, miR-19b or miR-16 does not, indicating that AGO3 has slicer activity but that this activity depends on the guide RNA. Our cleavage assays using chimeric guides revealed the significance of seed sequence for AGO3 activity, which depends specifically on the sequence of the post-seed. Unlike AGO2, target cleavage by AGO3 requires both 5'- and 3'-flanking regions. Our 3.28 Å crystal structure shows that AGO3 forms a complete active site mirroring that of AGO2, but not a well-defined nucleic acid-binding channel. These results demonstrating that AGO3 also has slicer activity but with more intricate substrate requirements, explain the observation that AGO3 has retained the necessary catalytic residues throughout its evolution. In addition, our structure inspires the idea that the substrate-binding channel of AGO3 and consequently its cellular function, may be modulated by accessory proteins.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-3
A, C
862Homo sapiensGene Names: AGO3 (EIF2C3)
Find proteins for Q9H9G7 (Homo sapiens)
Go to Gene View: AGO3
Go to UniProtKB:  Q9H9G7
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')B13Insect cell expression vector pTIE1
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')D15Insect cell expression vector pTIE1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 68.414α = 90.00
b = 68.414β = 90.00
c = 408.802γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
The Ohio State UniversityUnited StatesStart-up
Department of Energy (United States)United StatesGUP-41799
Department of Energy (United States)United StatesGUP-51294
JSTJapanJPMJPR13L7
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM124320

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references
  • Version 1.3: 2017-12-06
    Type: Author supporting evidence