Human Argonaute4 bound to guide RNA

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters.

Park, M.S.Araya-Secchi, R.Brackbill, J.A.Phan, H.D.Kehling, A.C.Abd El-Wahab, E.W.Dayeh, D.M.Sotomayor, M.Nakanishi, K.

(2019) Mol Cell 75: 725-740.e6

  • DOI: https://doi.org/10.1016/j.molcel.2019.06.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Despite the relevance of Argonaute proteins in RNA silencing, little is known about the structural steps of small RNA loading to form RNA-induced silencing complexes (RISCs). We report the 1.9 Å crystal structure of human Argonaute4 with guide RNA. Comparison with the previously determined apo structure of Neurospora crassa QDE2 revealed that the PIWI domain has two subdomains. Binding of guide RNA fastens the subdomains, thereby rearranging the active-site residues and increasing the affinity for TNRC6 proteins. We also identified two water pockets beneath the nucleic acid-binding channel that appeared to stabilize the mature RISC. Indeed, mutating the water-pocket residues of Argonaute2 and Argonaute4 compromised RISC assembly. Simulations predict that internal water molecules are exchangeable with the bulk solvent but always occupy specific positions at the domain interfaces. These results suggest that after guide RNA-driven conformational changes, water-mediated hydrogen-bonding networks tie together the converged domains to complete the functional RISC structure.

  • Organizational Affiliation

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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein argonaute-4863Homo sapiensMutation(s): 0 
Gene Names: AGO4EIF2C4KIAA1567
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCK5 (Homo sapiens)
Explore Q9HCK5 
Go to UniProtKB:  Q9HCK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCK5
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')12Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.98α = 90
b = 68.011β = 102.68
c = 83.27γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesGUP-41799
Japan Science and TechnologyJapanJPMJPR13L7
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM124320
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2021-03-10
    Changes: Structure summary
  • Version 1.4: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description