5Z9X

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.

Chen, J.Liu, L.You, C.Gu, J.Ruan, W.Zhang, L.Gan, J.Cao, C.Huang, Y.Chen, X.Ma, J.

(2018) Nat Commun 9: 3585-3585

  • DOI: 10.1038/s41467-018-05942-7
  • Primary Citation of Related Structures:  
    5Z9X, 5Z9Z

  • PubMed Abstract: 
  • A family of DEDDh 3'→5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residu ...

    A family of DEDDh 3'→5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3' end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3' end trimming mechanism for 3'→5' exonucleases in the metabolism of small non-coding RNAs.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. majb@fudan.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small RNA degrading nuclease 1A409Arabidopsis thalianaMutation(s): 0 
Gene Names: SDN1At3g50100F3A4.180
EC: 3.1
Find proteins for A3KPE8 (Arabidopsis thaliana)
Explore A3KPE8 
Go to UniProtKB:  A3KPE8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3')R10Arabidopsis thaliana
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download CCD File 
    A, R
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.252 
    • R-Value Observed: 0.253 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 87.993α = 90
    b = 87.993β = 90
    c = 178.639γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data collection
    Cootmodel building
    PHENIXphasing
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Natural Science Foundation of ChinaChinaNSFC 31230041

    Revision History 

    • Version 1.0: 2018-06-27
      Type: Initial release
    • Version 1.1: 2018-10-03
      Changes: Data collection, Database references