5XQ2

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

Sheng, G.Gogakos, T.Wang, J.Zhao, H.Serganov, A.Juranek, S.Tuschl, T.Patel, D.J.Wang, Y.

(2017) Nucleic Acids Res. 45: 9149-9163

  • DOI: 10.1093/nar/gkx547
  • Primary Citation of Related Structures:  5XOU, 5XOW

  • PubMed Abstract: 
  • We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies ...

    We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6'U7' and 6'A7' on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6'N7' bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson-Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction.


    Organizational Affiliation

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TtAgo (D546N)
A, B
685Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)N/A
Find proteins for Q746M7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q746M7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')X,E22Thermus thermophilus
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')Y,F19Thermus thermophilus
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*T)-3')C,D3Thermus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
E, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 201.843α = 90.00
b = 201.843β = 90.00
c = 201.843γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data processing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Natural Science Foundation of ChinaChina31571335
Natural Science Foundation of ChinaChina31630015
Natural Science Foundation of ChinaChina91440201
Chinese Ministry of Science and TechnologyChina2014CB910102

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release